[Freesurfer] mri_volsynth
Hi Freesurfers, I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10) I used the following command line to create the volume but I don't know how to choose it is position in scanner space. mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii I have the following question because i didn't find enough information in FS wiki about this command: 1. If the flag --dim (nc nr ns nf) is reffering to the volume dimentions. What is the fourth number (nf ) is standing for ? 2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ? 3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels? Thanks in advance , John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_volsynth
Thank you for the quick response. I wanted to create volume has the following dimentions in mm ( 6.25 X 6.25 X 7.5) in a position where the coordinates (in mm) are X=-15 Y= -4 Z= 13 is this command line correct: mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, August 31, 2015 at 11:30 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_volsynth some of this is answered if you run the command with --help On 8/31/15 3:33 PM, John Anderson wrote: Hi Freesurfers, I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10) I used the following command line to create the volume but I don't know how to choose it is position in scanner space. mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii I have the following question because i didn't find enough information in FS wiki about this command: 1. If the flag --dim (nc nr ns nf) is reffering to the volume dimentions. What is the fourth number (nf ) is standing for ? Number of frames (the time dimension) 2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ? How big the voxel is in mm 3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels? The "center" of the volume in mm, where "center" is defined as (Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices. Thanks in advance , John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_volsynth
Thank you! Actually when I run mri_volsynth --help I can't find --revol. is it the same flag --res? also what is the relationship between --dim and --volres? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, August 31, 2015 at 4:06 PM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_volsynth No, you will need to decide how big you want your voxels to be. If you use --volres 1 1 1 1 then that should work. It will put the center of the volume at that coordiate. If you want a single voxel, then use --dim 1 1 1 1 and --volres 6.25 6.25 7.5 1 On 8/31/15 7:52 PM, John Anderson wrote: Thank you for the quick response. I wanted to create volume has the following dimentions in mm ( 6.25 X 6.25 X 7.5) in a position where the coordinates (in mm) are X=-15 Y= -4 Z= 13 is this command line correct: mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, August 31, 2015 at 11:30 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_volsynth some of this is answered if you run the command with --help On 8/31/15 3:33 PM, John Anderson wrote: Hi Freesurfers, I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10) I used the following command line to create the volume but I don't know how to choose it is position in scanner space. mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii I have the following question because i didn't find enough information in FS wiki about this command: 1. If the flag --dim (nc nr ns nf) is reffering to the volume dimentions. What is the fourth number (nf ) is standing for ? Number of frames (the time dimension) 2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ? How big the voxel is in mm 3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels? The "center" of the volume in mm, where "center" is defined as (Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices. Thanks in advance , John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_volsynth
Perfect! Thank you very much for your help. Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, August 31, 2015 at 4:30 PM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_volsynth sorry, --res (not --volres). res is the voxel size (volume resolution). dim is the number of voxels in each dimension On 8/31/15 10:16 PM, John Anderson wrote: Thank you! Actually when I run mri_volsynth --help I can't find --revol. is it the same flag --res? also what is the relationship between --dim and --volres? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, August 31, 2015 at 4:06 PM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_volsynth No, you will need to decide how big you want your voxels to be. If you use --volres 1 1 1 1 then that should work. It will put the center of the volume at that coordiate. If you want a single voxel, then use --dim 1 1 1 1 and --volres 6.25 6.25 7.5 1 On 8/31/15 7:52 PM, John Anderson wrote: Thank you for the quick response. I wanted to create volume has the following dimentions in mm ( 6.25 X 6.25 X 7.5) in a position where the coordinates (in mm) are X=-15 Y= -4 Z= 13 is this command line correct: mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, August 31, 2015 at 11:30 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_volsynth some of this is answered if you run the command with --help On 8/31/15 3:33 PM, John Anderson wrote: Hi Freesurfers, I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10) I used the following command line to create the volume but I don't know how to choose it is position in scanner space. mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii I have the following question because i didn't find enough information in FS wiki about this command: 1. If the flag --dim (nc nr ns nf) is reffering to the volume dimentions. What is the fourth number (nf ) is standing for ? Number of frames (the time dimension) 2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ? How big the voxel is in mm 3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels? The "center" of the volume in mm, where "center" is defined as (Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices. Thanks in advance , John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] recon-all
Hi freesurfers, I am interested in studying the difference between the outer and deep white matter volume in my study groups. I am thinking in the following procedures: 1. If there is any way in Freesurfer to do segmentation for the white matter (only in the depth of 3 cm) starting from the cortex. Then second segmentation for the deep white matter. 2. Creating a mask ( using mri_binarize) for all the superficial white matter Freesurfer's labels and another mask for the deep white matter ( how can I find the Freesurfer deep white matter labels and the outer white matter labels ?) 3. If there is any atlas that can separate the outer and deep white matter then do the segmentation depending on this new atlas. Thanks in advance for any suggestion, John Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Segmenting deep and outer white matter
Hi Freesurfers, I am interested in studying the difference between the outer and deep white matter volume in my study groups. I am thinking in the following procedures: 1. If there is any way in Freesurfer to do segmentation for the white matter (only in the depth of 3 cm) starting from the cortex. Then second segmentation for the deep white matter. Is this possible in Freesurfer? 2. Creating a mask ( using mri_binarize) for all the superficial white matter Freesurfer's labels and another mask for the deep white matter ( how can I find the Freesurfer deep white matter labels and the outer white matter labels ?) 3. If there is any atlas that can separate the outer and deep white matter then running recon-all depending on this new atlas. Thanks in advance for any suggestion. John Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Segmenting deep and outer white matter
Hi Bruce, Thank you for your response! Actually, after reviewing multiple papers ( segmentation in Freesurfer) I found that using "wmparc.mgz" as an input in the command "mri_binarize" will enable me to create two mask ( depending on the white matter parcellate mentioned in wmparc.mgz): The first mask is for deep white matter and the second mask is for the outer white matter. I am facing one problem right now. I don't know how to divide the white matter parcellates mentioned in "wmparc.mgz" into deep and outer parcellates. Is there any reference that can help. The number of the parcellate is very big and for the purposes of publication I need a reference to divide them. Any help is highly appreciated. Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Saturday, September 05, 2015 at 4:23 PM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] Segmenting deep and outer white matter Hi John sorry, meant to respond but spaced it. Have you checked out the wmparc.mgz? It may have what you need. cheers Bruce On Sat, 5 Sep 2015, John Anderson wrote: > Hi Freesurfers, > I am interested in studying the difference between the outer and deep white > matter volume in my study groups. > > I am thinking in the following procedures: > 1. If there is any way in Freesurfer to do segmentation for the white matter > (only in the depth of 3 cm) starting from the cortex. Then second > segmentation for the deep white matter. Is this possible in Freesurfer? > 2. Creating a mask ( using mri_binarize) for all the superficial white > matter Freesurfer's labels and another mask for the deep white matter ( how > can I find the Freesurfer deep white matter labels and the outer white > matter labels ?) > 3. If there is any atlas that can separate the outer and deep white matter > then running recon-all depending on this new atlas. > > Thanks in advance for any suggestion. > John > > > Bests, > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Segmenting deep and outer white matter
Hi Doug, Thank you for your response. When we open "wmparc.mgz" in freeview we can see clearly that we have labels for cortical parcellations and it is white matter parcellations as well as the unsegmented white matter What is really confusing me is that deep structures like the thalamus, amygdala, putamen, caudate, hypocampus .etc are also labeled in "wmparc.mgz". Are these labels means the white matter part of these segments or it is gray and white matter together like the segments mentioed in "aseg.mgz" ?! Please see the attached list of labels for one of my subjects. Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, September 07, 2015 at 1:02 PM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmenting deep and outer white matter The best thing is to take a look at the wmparc. It was not really designed to be deep and superficial. There is only one "deep" WM seg which is called "Unsgemented White Matter" or something like that. doug On 9/5/15 5:54 PM, Bruce Fischl wrote: Hi John I defer to Doug. Not sure he ever published it though Bruce On Sat, 5 Sep 2015, John Anderson wrote: Hi Bruce, Thank you for your response! Actually, after reviewing multiple papers ( segmentation in Freesurfer) I found that using "wmparc.mgz" as an input in the command "mri_binarize" will enable me to create two mask ( depending on the white matter parcellate mentioned in wmparc.mgz): The first mask is for deep white matter and the second mask is for the outer white matter. I am facing one problem right now. I don't know how to divide the white matter parcellates mentioned in "wmparc.mgz" into deep and outer parcellates. Is there any reference that can help. The number of the parcellate is very big and for the purposes of publication I need a reference to divide them. Any help is highly appreciated. Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Saturday, September 05, 2015 at 4:23 PM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] Segmenting deep and outer white matter Hi John sorry, meant to respond but spaced it. Have you checked out the wmparc.mgz? It may have what you need. cheers Bruce On Sat, 5 Sep 2015, John Anderson wrote: > Hi Freesurfers, > I am interested in studying the difference between the outer and deep white > matter volume in my study groups. > > I am thinking in the following procedures: > 1. If there is any way in Freesurfer to do segmentation for the white matter > (only in the depth of 3 cm) starting from the cortex. Then second > segmentation for the deep white matter. Is this possible in Freesurfer? > 2. Creating a mask ( using mri_binarize) for all the superficial white > matter Freesurfer's labels and another mask for the deep white matter ( how > can I find the Freesurfer deep white matter labels and the outer white > matter labels ?) > 3. If there is any atlas that can separate the outer and deep white matter > then running recon-all depending on this new atlas. > > Thanks in advance for any suggestion. > John > > > Bests, > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact
[Freesurfer] White matter volume
Hi Bruce, Kindly I want to inquire about the difference between white matter volume generated by freesurfer ( specifically the white matter parcellations volume mentioned in wmparc.stats) and the vwhite matter volume generated by other tools like fslstats. For example: If I use a binarized mask from wmparc.mgz for the precentral gyrus in the command : fslstats -i MPRAGE.nii.gz ( reoriented and skull stripped) -k -V Then What is the differecne between this volume generated by "fslstats" and the precenral gyrus volume mentioned in wmparc.stats. Which one is more accurate? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 4and the white matter volume generated by other methods like using fslstats19 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tracula_weighted dti metrics values
Hi Anastasia, How the script "dmri_pathstats" compute the weighted FA, MD, AD, and RD values? I checked the command "dmri_pathstats" inside the file "trac-all.log" but I was unable to figure out how this weighting is working. Is it by multiplying the mean DTI metrics by the number of voxel? If my FA maps is "dtifit_FA.nii.gz" and my probabilistic distribution map for the cortico spinal tract is "path.pd.nii.gz" and I want to compute FA value using the command "fslstats" like: fslstats dtifit_FA.nii.gz -k path.pd.nii.gz -m >This command will output the mean FA for the probabilistic distribution map. How can I weight this FA value using the previous command line? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Basal ganglia
Hi Experts, I want to do tractography for the cortico spinal tract between two ROIs ( ROI1: precentral gyrus; ROI2: basal ganglia). I created the first ROI using mask form wmparc.mgz. How can I create mask for the basal ganglia ( there is no label for it). Do I need to segmenta the basal ganglia separatly? Is there any tool in Freesurfer that can help? Thanks for any suggestion. Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Break 3D volume
Dear FS Experts, Are there any tools in Freesurfer or Matlab scripts that can help to break down a 3D volume ( created using mri_volsynth) to a multiple equal sub volumes ( like the attached figure ) Thanks in a dvance for any suggestion! John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Break 3D volume
Hi Bruce, Thank you for the quick response. it is really highly appreciated! I have 3D mask in the form of nifti file and it has the shape of large square( the black big square in my figure). I wanted to divid it to a smaller and equale volumes. It iseems that mri_extract can support my objectives: Please how can I use this command. I was unable to find any instructions: If my 3D maks is "mask.nii" and the command is mri_extract x0 y0 z0 dx dy dz how can I use the command properly? : is this where my file is located? x0 y0 z0 dx dy dz: What I should use here? Thank you very much for your help John Sent: Wednesday, June 08, 2016 at 9:13 AM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] Break 3D volume Hi John I'm not exactly sure what you mean, but you can use mri_extract to pull out rectangular subvolumes. cheers Bruce On Wed, 8 Jun 2016, John Anderson wrote: > Dear FS Experts, > Are there any tools in Freesurfer or Matlab scripts that can help to break > down a 3D volume ( created using mri_volsynth) to a multiple equal sub > volumes ( like the attached figure ) > Thanks in a dvance for any suggestion! > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > > > > [IMAGE] > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Break 3D volume
Thank you Bruce... This is very helpful! Bests, John Sent: Wednesday, June 08, 2016 at 9:32 AM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] Break 3D volume the help is old! should be . (x0,y0,z0) is the starting point of your bounding box, and (dx,dy,dz) is the extent of it (in voxels) On Wed, 8 Jun 2016, John Anderson wrote: > Hi Bruce, > Thank you for the quick response. it is really highly appreciated! > I have 3D mask in the form of nifti file and it has the shape of large > square( the black big square in my figure). I wanted to divid it to a > smaller and equale volumes. It iseems that mri_extract can support my > objectives: > Please how can I use this command. I was unable to find any instructions: > If my 3D maks is "mask.nii" and the command is mri_extract x0 y0 > z0 dx dy dz how can I use the command properly? > : is this where my file is located? > x0 y0 z0 dx dy dz: What I should use here? > > Thank you very much for your help > > > John > Sent: Wednesday, June 08, 2016 at 9:13 AM > From: "Bruce Fischl" > To: "Freesurfer support list" > Subject: Re: [Freesurfer] Break 3D volume > Hi John > > I'm not exactly sure what you mean, but you can use mri_extract to pull > out rectangular subvolumes. > > cheers > Bruce > On Wed, 8 Jun 2016, John Anderson wrote: > > > Dear FS Experts, > > Are there any tools in Freesurfer or Matlab scripts that can help to break > > down a 3D volume ( created using mri_volsynth) to a multiple equal sub > > volumes ( like the attached figure ) > > Thanks in a dvance for any suggestion! > > John Anderson > > > > Senior Research Associate > > Psychological and Brain Sciences Dept. > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > > Phone: +1 (603) 646-9834 > > Fax: +1 (603) 646-1419 > > > > > > > > [IMAGE] > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] smoothing T1 images
Hi FS experts, I have T1 images with low quality (noise and artifacts). I am wondering if smoothing these images, before runing the command "Recon-all", can help to improve the segmentation and parcellation process for these images. Thanks for any advice! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Qdec-correction for multiple comparison
Dear FS experts, I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison. In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend montecarlo or FDR. Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo) Thank you very much for any comment! John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Qdec-correction for multiple comparison
Dear FS experts, I will re post this thread again looking for your help and support: I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison. In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend to correct the results of cortical thickness analysis? Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo) Thank you very much for any comment! John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Qdec-correction for multiple comparison
Dear FS experts, I will re post this thread again looking for your help and support: I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison. In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend to correct the results of cortical thickness analysis? Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo) Thank you very much for any comment! John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Qdec-correction for multiple comparison
Hi Doug, I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison. In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend to correct the results of cortical thickness analysis? Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo) Thank you very much for any comment! John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Qdec-correction for multiple comparison
Hi Doug, thank you veru much for the answr. Please what do you mean by " an emperical question that depends on your data"? For example: I have two groups of participants. I ran cortical thickness analysis in Qdec to study the differnce between the groups in cortical thickness: 1. Monte carlo simulation reported differnce between the groups ( p<0.05 ) in the precentral gyrus and the paracentral gyrus 2. FDR reported no diffwernce between the groups ( p<0.05) Depending on pathology. I expect a differnce in the orecentral gyrus. How can I explain the results of FDR and mote carlo simulation? Does "empirical " means to follow the results that support the hypothesis? John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Wednesday, July 06, 2016 at 1:44 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec-correction for multiple comparison There is no recommendation between FDR and monte carlo. The question of which one is "better" is an emperical question that depends on your data. On 06/29/2016 06:38 AM, John Anderson wrote: > Dear FS experts, > I will re post this thread again looking for your help and support: > I ran cortical thickness analysis between two groups using Qdec and I > want to correct the results for multiple comparison. > In Qdec there are two choices to correct the data for multiple > comparison (FDR and montecarlo) . Which method do you recommend to > correct the results of cortical thickness analysis? Are there any > rules that I need to follow when I choose my method to correct the > results for multiple comparison ( i.e FDR or montecarlo) > Thank you very much for any comment! > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] white and gray matter masks
Dear FS experts, I need to crate a mask for whole white matter in the brain including the cerebellum. Also I need a mask for the whoe gray matter. Can I binzarize ( i.e. use mri_binarize) and input the files: wm.seg.mgz from the output of recon-all to create a a mask for global white matter and the file ribbon.mgz the output of recon-all to create a a mask for global gray matter Thank you for any advice! Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] QA tools
Hello, FS experts, I am trying to use QA tool: I ran the following command recon_checker -snaps-only -s-file subjects.txt The script output the following: X11 connection rejected because of wrong authentication. GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0 X11 connection rejected because of wrong authentication. GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0 X11 connection rejected because of wrong authentication. GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0 Taking snapshots for subject ALS-0038 X11 connection rejected because of wrong authentication. GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0 X11 connection rejected because of wrong authentication. GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0 X11 connection rejected because of wrong authentication. GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0 At the end it said that he process finshed. I checked the AQ folder and the snaps where not there Any suggestions! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Volume or surface?
Dear FS experts, I want to know what is the output (volume or surface) of the following scripts. (The input is file.nii.gz which is a volumetric ) 1. spmregister --s subj --mov file.nii.gz --reg reg.dat --o file_t1.mgh #is the output file (file_t1.mgh) is a volume or a surface 2. mris_preproc --target fsaverage --hemi lh --projfrac 0.5 --iv file1_t1.mgh reg1.dat --iv file2_t1.mgh reg --out lh.mgh #is the output file (lh.mgh) is a volume or a surface where I must feed the output of "mris_preproc"? to "mri_vol2surf or mri_surf2surf Thank you for your help Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] surface based analysis for subcortical structures
Dear experts, I ran surface based analysis using PET maps. As the following: spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir then mri_glmfit-sim to correct for multiple comparison. I want to study the subcortical regions and map it on MNI305. How can I resume tha analysis for subcortical structures? Thank you for any help! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] de-identify DICOM
Hi FS experts, I wanted to inquire if there are any tools in FS that can help to de-identify DICOMs? Thank you for any comment John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] surface based analysis for subcortical structures
Dear Doug, Thank you very much for this detailed explaination. I highly appreciate your help Kindly I have the following question: The command mri_vol2vol ran smoothly without any errors The command mri_mask output the following : mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz suvr.tal2mm.subc.nii freadFloat: fread failed DoAbs = 0 Writing masked volume to suvr.tal2mm.subc.nii...done. Should I worry about this error ? I ignored this error and I continued the following steps. They went fine but when I correct for multiple comparisons using the command "mri_glmfit-sim" I get the following: mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir log file is subc.glmdir/cache.mri_glmfit-sim.log cd /analyses/pet_scan/SBM/sm /usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Thu Oct 20 21:10:31 EDT 2016 Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux malshikh setenv SUBJECTS_DIR /analyses/recons FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Original mri_glmfit command line: cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 10.682767 ERROR: cannot find /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd I smoothed just fwhm = 1 Kindly how can I troubleshoo? thank you for any advice Bests, John Sent: Thursday, October 20, 2016 at 12:16 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis for subcortical structures After spmregister, you can run mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii # mask out the cortical structures mri_mask pet.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz pet.tal2mm.subc.nii # Concatenate all subjects together mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o all.pet.tal2mm.subc.nii --prune # smooth mri_fwhm --i all.pet.tal2mm.subc.nii --mask $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X --smooth-only --o all.pet.tal2mm.subc.smoothed.nii mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C 2gc0.mtx --glmdir subc.glmdir On 10/19/2016 05:09 PM, John Anderson wrote: > Dear experts, > I ran surface based analysis using PET maps. As the following: > spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh > mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh > mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh > mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir// > then mri_glmfit-sim to correct for multiple comparison. > I want to study the subcortical regions and map it on MNI305. How can > I resume tha analysis for subcortical structures? > Thank you for any help! > Bests, > John > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partner
[Freesurfer] Fw: Re: surface based analysis for subcortical structures
Thank you very much Doug, The codes worked very well. I was using the wrong command to correct the data. My command was mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces and for subcortical structures it must be mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166 All the bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Thursday, October 20, 2016 at 9:20 PM From: "John Anderson" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis for subcortical structures Dear Doug, Thank you very much for this detailed explaination. I highly appreciate your help Kindly I have the following question: The command mri_vol2vol ran smoothly without any errors The command mri_mask output the following : mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz suvr.tal2mm.subc.nii freadFloat: fread failed DoAbs = 0 Writing masked volume to suvr.tal2mm.subc.nii...done. Should I worry about this error ? I ignored this error and I continued the following steps. They went fine but when I correct for multiple comparisons using the command "mri_glmfit-sim" I get the following: mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir log file is subc.glmdir/cache.mri_glmfit-sim.log cd /analyses/pet_scan/SBM/sm /usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Thu Oct 20 21:10:31 EDT 2016 Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux malshikh setenv SUBJECTS_DIR /analyses/recons FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Original mri_glmfit command line: cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 10.682767 ERROR: cannot find /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd I smoothed just fwhm = 1 Kindly how can I troubleshoo? thank you for any advice Bests, John Sent: Thursday, October 20, 2016 at 12:16 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis for subcortical structures After spmregister, you can run mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii # mask out the cortical structures mri_mask pet.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz pet.tal2mm.subc.nii # Concatenate all subjects together mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o all.pet.tal2mm.subc.nii --prune # smooth mri_fwhm --i all.pet.tal2mm.subc.nii --mask $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X --smooth-only --o all.pet.tal2mm.subc.smoothed.nii mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C 2gc0.mtx --glmdir subc.glmdir On 10/19/2016 05:09 PM, John Anderson wrote: > Dear experts, > I ran surface based analysis using PET maps. As the following: > spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh > mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh > mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh > mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir// > then mri_glmfit-sim to correct for multiple comparison. > I want to study the subcortical regions and map it on MNI305. How can > I resume tha analysis for subcortical structures? > Thank you for any help! > Bests, > John > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom
Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures
Hi Doug, Yes! Thank you for the offer to share the script. Actually I want to run surface based analysis for sub cortical structres I tried the command mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces But it failed (I don't know why!) and this is the reason why I want to use "mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166" Bests, John Sent: Friday, October 28, 2016 at 11:53 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures If you want to use GRF, then I should get you new versions of some of the programs as the volume-based GRF used the Friston 1994 algorithm that was not as accurate as the Worsley 1996 algorithm. I just updated my code last week (better late than never:). But in the end, you probably want to use permutation if your group analysis allows it. On 10/23/16 10:25 AM, John Anderson wrote: Thank you very much Doug, The codes worked very well. I was using the wrong command to correct the data. My command was mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces and for subcortical structures it must be mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166 All the bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Thursday, October 20, 2016 at 9:20 PM From: "John Anderson" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis for subcortical structures Dear Doug, Thank you very much for this detailed explaination. I highly appreciate your help Kindly I have the following question: The command mri_vol2vol ran smoothly without any errors The command mri_mask output the following : mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz suvr.tal2mm.subc.nii freadFloat: fread failed DoAbs = 0 Writing masked volume to suvr.tal2mm.subc.nii...done. Should I worry about this error ? I ignored this error and I continued the following steps. They went fine but when I correct for multiple comparisons using the command "mri_glmfit-sim" I get the following: mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir log file is subc.glmdir/cache.mri_glmfit-sim.log cd /analyses/pet_scan/SBM/sm /usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Thu Oct 20 21:10:31 EDT 2016 Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux malshikh setenv SUBJECTS_DIR /analyses/recons FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Original mri_glmfit command line: cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 10.682767 ERROR: cannot find /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd I smoothed just fwhm = 1 Kindly how can I troubleshoo? thank you for any advice Bests, John Sent: Thursday, October 20, 2016 at 12:16 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis for subcortical structures After spmregister, you can run mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii # mask out the cortical structures mri_mask pet.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz pet.tal2mm.subc.nii # Concatenate all subjects together mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o all.pet.tal2mm.subc.nii --prune # smooth mri_fwhm --i all.pet.tal2mm.subc.nii --mask $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X --smooth-only --o all.pet.tal2mm.subc.smoothed.nii mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C 2gc0.mtx --glmdir subc.glmdir On 10/19/2016 05:09 PM, John Anderson wrote: > Dear experts, > I ran surface based analysis using PET maps. As the following: > spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh > mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh > mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh > mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir// > t
Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures
Hi Doug, I want to use GRF. Will you be willing to share the new versions of the programs? Your help is highly appreciated. Thanks! Jon on: Friday, October 28, 2016 at 11:53 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures If you want to use GRF, then I should get you new versions of some of the programs as the volume-based GRF used the Friston 1994 algorithm that was not as accurate as the Worsley 1996 algorithm. I just updated my code last week (better late than never:). But in the end, you probably want to use permutation if your group analysis allows it. On 10/23/16 10:25 AM, John Anderson wrote: Thank you very much Doug, The codes worked very well. I was using the wrong command to correct the data. My command was mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces and for subcortical structures it must be mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166 All the bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Thursday, October 20, 2016 at 9:20 PM From: "John Anderson" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis for subcortical structures Dear Doug, Thank you very much for this detailed explaination. I highly appreciate your help Kindly I have the following question: The command mri_vol2vol ran smoothly without any errors The command mri_mask output the following : mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz suvr.tal2mm.subc.nii freadFloat: fread failed DoAbs = 0 Writing masked volume to suvr.tal2mm.subc.nii...done. Should I worry about this error ? I ignored this error and I continued the following steps. They went fine but when I correct for multiple comparisons using the command "mri_glmfit-sim" I get the following: mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir log file is subc.glmdir/cache.mri_glmfit-sim.log cd /analyses/pet_scan/SBM/sm /usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Thu Oct 20 21:10:31 EDT 2016 Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux malshikh setenv SUBJECTS_DIR /analyses/recons FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Original mri_glmfit command line: cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 10.682767 ERROR: cannot find /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd I smoothed just fwhm = 1 Kindly how can I troubleshoo? thank you for any advice Bests, John Sent: Thursday, October 20, 2016 at 12:16 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis for subcortical structures After spmregister, you can run mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii # mask out the cortical structures mri_mask pet.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz pet.tal2mm.subc.nii # Concatenate all subjects together mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o all.pet.tal2mm.subc.nii --prune # smooth mri_fwhm --i all.pet.tal2mm.subc.nii --mask $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X --smooth-only --o all.pet.tal2mm.subc.smoothed.nii mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C 2gc0.mtx --glmdir subc.glmdir On 10/19/2016 05:09 PM, John Anderson wrote: > Dear experts, > I ran surface based analysis using PET maps. As the following: > spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh > mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh > mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh > mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir// > then mri_glmfit-sim to correct for multiple comparison. > I want to study the subcortical regions and map it on MNI305. How can > I resume tha analysis for subcortical structures? > Thank you for any help! > Bests, > John > > > _
[Freesurfer] recon all
Dear Freesurfer experts, I ran the following command on a T1 image recon-all -subjid 089 -all -qcache and I got the following error message: talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050) I highly appreciate an explanation for the meaning of this error and how to fix it. Best John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon all
Thank you very much Doug, Kindly, what do you suggest me to use instead of fslswapidim. What is your choice in this case? I highly appreciate your experience ! Bests, John Sent: Friday, November 11, 2016 at 4:42 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all On this volume as the head is almost at a 45deg angle perhaps causing the nominal SI and AP to swap. Even after swap dim, the angle is pretty extreme, but maybe better than the original so the tal check does not fail. In general, I don't like to use swapdim as I'm afraid that it might left-right rev the volume. In either case, you can manually check the tal reg to see if it looks ok. On 11/11/2016 03:56 PM, John Anderson wrote: > Thank you Doug, > Attched are to snapshots > #1 is for the original T1 ( i.e. as aquired) and this image what > output the error message mentioned in my previous email. > #2 is after correcting the orientation using the command "*fslswapdim > 001.nii RL PA IS T1-2mm_orientOK.nii"* > I re run the same command "recon-all" on the newly corrected T1 image. > The analysis is runnig fine right now, but when I checked the file > "recon-all" I found similar error to what terminated my previous > analysis. The differnce here is that the analysis didn't fail! > Here is what I have in "recon.log" > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0386, pval=0.0034 < threshold=0.0050) > INFO: Attempting MINC mritotal to perform Talairach align > Do I need to warry about this error? I appreciate any suggestion to > improve analyzing this image. > Bests, > John > *Sent:* Friday, November 11, 2016 at 3:19 PM > *From:* "Douglas N Greve" > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] recon all > This can also happen if the head is oriented in a strange way. This can > happen with older patients that tend to tilt their head back. > > > On 11/10/2016 08:27 PM, Bruce Fischl wrote: > > Hi John > > > > it means that the talairach transform that was computed was extremely > > unlikely and deemed to be probably incorrect. Frequently this happens > > if you start with images (like analyze) that don't contain accurate > > direction cosine information. You can check this by bringing one of > > the volumes in freeview and checking to make sure that the anatomical > > directions we show > > (e.g. anterior/posterior) correspond to the true anatomy. Sometimes > > abnormal anatomiies like huge ventricles can also make it fail, but > > you need to figure out which one it is before deciding what to do > > > > cheers > > Bruce > > > > > > On Fri, 11 Nov 2016, John Anderson wrote: > > > >> Dear Freesurfer experts, > >> I ran the following command on a T1 image > >> recon-all -subjid 089 -all -qcache > >> > >> and I got the following error message: > >> > >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm > >> > >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > >> ***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050) > >> > >> > >> I highly appreciate an explanation for the meaning of this error and > >> how to > >> fix it. > >> > >> > >> Best > >> John > >> > >> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent t
[Freesurfer] dtrecon
Dear Freesurfer experts, I want to analyze DTI data using the command dt_recon --i dwi.nii --b bvals bvecs --s subj1 --o /subj1 Under Fressurfer 5.3, the analysis fail showing this error message: nifti1Read(): unsupported slice timing pattern 5 in /data/anaconda/mesgp/dtrecon3/subj1/dwi.nii I re-run the same previous comand line under freesurfer 6 and the nalysis went fine. The problem is that all my recons are prepared under freesurfer 5.3. If I use dt_recon under FS6 does this affect the results? Thank you for any advice you provide! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures
Thank you very much Doug. You are so awsome :) Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, November 14, 2016 at 1:00 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures Hi, I just found a bug in mri_glmfit-sim in regards to GRF on volume-based data. I put a fixed version at the same location. Please use the new version On 11/04/2016 10:25 AM, Douglas N Greve wrote: > oops, sorry, > > download these files > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_volcluster > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster > > Copy them into $FREESURFER_HOME/bin (after making a backup of the > previous files). > > Edit mri_glmfit-sim to remove > > source $FREESURFER_HOME/sources.csh > > then hopefully everything should work > > doug > > > On 11/04/2016 06:11 AM, John Anderson wrote: >> Hi Doug, >> I want to use GRF. Will you be willing to share the new versions of >> the programs? Your help is highly appreciated. >> Thanks! >> Jon >> *on:* Friday, October 28, 2016 at 11:53 AM >> *From:* "Douglas Greve" >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] Fw: Re: surface based analysis for >> subcortical structures >> >> If you want to use GRF, then I should get you new versions of some of >> the programs as the volume-based GRF used the Friston 1994 algorithm >> that was not as accurate as the Worsley 1996 algorithm. I just >> updated my code last week (better late than never:). But in the end, >> you probably want to use permutation if your group analysis allows it. >> >> On 10/23/16 10:25 AM, John Anderson wrote: >> >> Thank you very much Doug, >> The codes worked very well. I was using the wrong command to >> correct the data. >> My command was >> mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 >> --3spaces >> and for subcortical structures it must be >> >> mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166 >> >> All the bests, >> John Anderson >> >> Senior Research Associate >> Psychological and Brain Sciences Dept. >> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH >> 03755 >> Phone: +1 (603) 646-9834 >> Fax: +1 (603) 646-1419 >> *Sent:* Thursday, October 20, 2016 at 9:20 PM >> *From:* "John Anderson" >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] surface based analysis for subcortical >> structures >> Dear Doug, >> Thank you very much for this detailed explaination. I highly >> appreciate your help >> Kindly I have the following question: >> The command mri_vol2vol ran smoothly without any errors >> The command mri_mask output the following : >> mri_mask suvr.tal2mm.nii >> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz >> suvr.tal2mm.subc.nii >> freadFloat: fread failed >> DoAbs = 0 >> Writing masked volume to suvr.tal2mm.subc.nii...done. >> Should I worry about this error ? >> I ignored this error and I continued the following steps. They >> went fine but when I correct for multiple comparisons using the >> command "mri_glmfit-sim" I get the following: >> mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 >> --3spaces >> cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat >> --C 2G0C.mtx --glmdir subc.glmdir >> log file is subc.glmdir/cache.mri_glmfit-sim.log >> cd /analyses/pet_scan/SBM/sm >> /usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim >> --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces >> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ >> Thu Oct 20 21:10:31 EDT 2016 >> Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 >> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux >> malshikh >> setenv SUBJECTS_DIR /analyses/recons >> FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 >> Original mri_glmfit command line: >> cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat >> --C 2G0C.mtx --glmdir subc.glmdir >> DoSim = 0 >> UseCache = 1 >> DoPoll = 0 >> DoPBSubmit = 0 >> DoBackground = 0 >> DiagCluster = 0 >> gd2mtx = dods >> fwhm = 10.682767 &g
[Freesurfer] Re: surface based analysis for subcortical structures
Hi Doug, I have one additional question regarding surface based analyses: Let's say that we have two types of brain lesions: 1. The first one is located in the cortical parcellates ( the labels in freesurfer atlas (wmparc.mgz) are named ctx-lh-? and ctx-rh-?). 2. The second lesion is located in the white matter parcellates ( the labels in freesurfer atlas (wmparc.mgz) are named wm-lh-? and wm-rh-?). Depedning on the location of these lesions the study subjects are divided into three groups ( normal people, those who have lesions in the cortical parcellates and those who have lesions in the white matter parcellates) I want to invistigate the position of these lesions by runnig two surface based analyses (using PET images and the pipelines mentioned bellow) to show the location of these lesions (superfecial and deeper): 1. The first surface based analysis is between normal people and those who have supperfecial lesions in the cortical parcellates 2. The second surface based analysis is betweem normal people and those who have deep lesions in the white matter parcellates In this case can the surface based analysis be able to find these differnces (between lesions in the cortical parcellates vs lesions in the white matter parcellates) using the same projection factor? Or I need to change the projection factor to include more deeper structures in the analysis? Thank you for any advice! John Sent: Monday, November 14, 2016 at 1:29 PM From: "John Anderson" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures Thank you very much Doug. You are so awsome :) Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, November 14, 2016 at 1:00 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures Hi, I just found a bug in mri_glmfit-sim in regards to GRF on volume-based data. I put a fixed version at the same location. Please use the new version On 11/04/2016 10:25 AM, Douglas N Greve wrote: > oops, sorry, > > download these files > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_volcluster > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster > > Copy them into $FREESURFER_HOME/bin (after making a backup of the > previous files). > > Edit mri_glmfit-sim to remove > > source $FREESURFER_HOME/sources.csh > > then hopefully everything should work > > doug > > > On 11/04/2016 06:11 AM, John Anderson wrote: >> Hi Doug, >> I want to use GRF. Will you be willing to share the new versions of >> the programs? Your help is highly appreciated. >> Thanks! >> Jon >> *on:* Friday, October 28, 2016 at 11:53 AM >> *From:* "Douglas Greve" >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] Fw: Re: surface based analysis for >> subcortical structures >> >> If you want to use GRF, then I should get you new versions of some of >> the programs as the volume-based GRF used the Friston 1994 algorithm >> that was not as accurate as the Worsley 1996 algorithm. I just >> updated my code last week (better late than never:). But in the end, >> you probably want to use permutation if your group analysis allows it. >> >> On 10/23/16 10:25 AM, John Anderson wrote: >> >> Thank you very much Doug, >> The codes worked very well. I was using the wrong command to >> correct the data. >> My command was >> mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 >> --3spaces >> and for subcortical structures it must be >> >> mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166 >> >> All the bests, >> John Anderson >> >> Senior Research Associate >> Psychological and Brain Sciences Dept. >> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH >> 03755 >> Phone: +1 (603) 646-9834 >> Fax: +1 (603) 646-1419 >> *Sent:* Thursday, October 20, 2016 at 9:20 PM >> *From:* "John Anderson" >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] surface based analysis for subcortical >> structures >> Dear Doug, >> Thank you very much for this detailed explaination. I highly >> appreciate your help >> Kindly I have the following question: >> The command mri_vol2vol ran smoothly without any errors >> The command mri_mask output the following : >>
[Freesurfer] surface based analysis (projfrac)
Dear FS experts, I am working on surface based analysis using freesurfer. I want to inquire about the flag "projfrac" in the command "mris_preproc" I ran voxel wise analysis including the same subjects. I found differnce between the groups in areas close to the corpus callosum. I want to get the same results using surface based analysis. If I use the projfrac=0.5 is this able to show the same results that I got in voxel wise analysis at the level of the corpus callosum. Do I need to use differnt number for projfrac ? Thank you for any advice. Best, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] surface based analysis (projfrac)
Thank you Doug, Exactly! I meant GM near the CC. When I used "projfrac=0.5 " there was no differnce between the groups at "cwp 0.05", and when I changed the "projfrac to 0" I got significant differnce between the groups in specific areas at "cwp 0.01". Kindly, how can this be explained? I highly appreciate if you help me to understand this point: For "projfrac =0" I expect the surface based analysis to be running close to white matter. Right? and when I used "projfrac=0.5" the analysis is running in the middle area between pial and white. When the analysis is not showing any differne between the groups for "projfrac 0.5" and showing differnce for "projfrac 0" that means the differnce between the groups is deeper and closer to white matter. Is this correct? Thank you for any input and clarification! Bests, John Sent: Tuesday, January 10, 2017 at 10:51 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis (projfrac) When you say in the corpus callosum, do you mean in WM? The surface-based analysis is only for cortical GM. If you mean in GM near the CC, then the analysis is appropriate. The projfrac parameter sets the sampling location between the white and pial surfaces where 0.5 means half way. On 1/10/17 8:07 AM, John Anderson wrote: Dear FS experts, I am working on surface based analysis using freesurfer. I want to inquire about the flag "projfrac" in the command "mris_preproc" I ran voxel wise analysis including the same subjects. I found differnce between the groups in areas close to the corpus callosum. I want to get the same results using surface based analysis. If I use the projfrac=0.5 is this able to show the same results that I got in voxel wise analysis at the level of the corpus callosum. Do I need to use differnt number for projfrac ? Thank you for any advice. Best, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] surface based analysis (projfrac)
Thank you very much Doug and thank you for briniging the issue of "partial volume effect " to my attention. Kindly, I have one last question. I found in wiki that the default values for projfrc value are between 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1, 2 ", In other words, less than zero means the surface based analysis is running at a lower level of the white matter. Can the issue of the partial volume effect be avoided by using larger numbers for "projfrac" ? Bests, John Sent: Thursday, January 12, 2017 at 5:08 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis (projfrac) yes, that is correct. However, understand that there might only be a difference of 1mm between those two locations, so it could easily be a partial volume effect On 01/11/2017 08:50 AM, John Anderson wrote: > Thank you Doug, > Exactly! I meant GM near the CC. > When I used "projfrac=0.5 " there was no differnce between the groups > at "cwp 0.05", and when I changed the "projfrac to 0" I got > significant differnce between the groups in specific areas at "cwp > 0.01". Kindly, how can this be explained? I highly appreciate if you > help me to understand this point: > For "projfrac =0" I expect the surface based analysis to > be running close to white matter. Right? and when I used > "projfrac=0.5" the analysis is running in the middle area between pial > and white. When the analysis is not showing any differne between the > groups for "projfrac 0.5" and showing differnce for "projfrac 0" that > means the differnce between the groups is deeper and closer to white > matter. Is this correct? > Thank you for any input and clarification! > Bests, > John > *Sent:* Tuesday, January 10, 2017 at 10:51 AM > *From:* "Douglas Greve" > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > > When you say in the corpus callosum, do you mean in WM? The > surface-based analysis is only for cortical GM. If you mean in GM near > the CC, then the analysis is appropriate. The projfrac parameter sets > the sampling location between the white and pial surfaces where 0.5 > means half way. > > On 1/10/17 8:07 AM, John Anderson wrote: > > Dear FS experts, > I am working on surface based analysis using freesurfer. I want to > inquire about the flag "projfrac" in the command "mris_preproc" > I ran voxel wise analysis including the same subjects. I found > differnce between the groups in areas close to the corpus > callosum. I want to get the same results using surface based > analysis. If I use the projfrac=0.5 is this able to show the same > results that I got in voxel wise analysis at the level of the > corpus callosum. Do I need to use differnt number for projfrac ? > Thank you for any advice. > > Best, > John > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The > information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and > the e-mail contains patient information, please contact the Partners > Compliance HelpLine at http://www.partners.org/complianceline . If the > e-mail was sent to you in error but does not contain patient > information, please contact the sender and properly dispose of the e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] surface based analysis (projfrac)
Thank you very much Doug, Kindly, do you suggest me any steps to avoid patial volume effects in surface based analyses ? Best, John Sent: Friday, January 13, 2017 at 12:21 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis (projfrac) On 01/12/2017 05:20 PM, John Anderson wrote: > Thank you very much Doug and thank you for briniging the issue of > "partial volume effect " to my attention. Kindly, I have one last > question. > I found in wiki that the default values for projfrc value are between > 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1, > 2 ", In other words, less than zero means the surface based analysis > is running at a lower level of the white matter. Yes > Can the issue of the partial volume effect be avoided by using larger > numbers for "projfrac" ? No, PVEs can't be avoided that way. > Bests, > John > *Sent:* Thursday, January 12, 2017 at 5:08 PM > *From:* "Douglas N Greve" > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > yes, that is correct. However, understand that there might only be a > difference of 1mm between those two locations, so it could easily be a > partial volume effect > > > On 01/11/2017 08:50 AM, John Anderson wrote: > > Thank you Doug, > > Exactly! I meant GM near the CC. > > When I used "projfrac=0.5 " there was no differnce between the groups > > at "cwp 0.05", and when I changed the "projfrac to 0" I got > > significant differnce between the groups in specific areas at "cwp > > 0.01". Kindly, how can this be explained? I highly appreciate if you > > help me to understand this point: > > For "projfrac =0" I expect the surface based analysis to > > be running close to white matter. Right? and when I used > > "projfrac=0.5" the analysis is running in the middle area between pial > > and white. When the analysis is not showing any differne between the > > groups for "projfrac 0.5" and showing differnce for "projfrac 0" that > > means the differnce between the groups is deeper and closer to white > > matter. Is this correct? > > Thank you for any input and clarification! > > Bests, > > John > > *Sent:* Tuesday, January 10, 2017 at 10:51 AM > > *From:* "Douglas Greve" > > *To:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > > > > When you say in the corpus callosum, do you mean in WM? The > > surface-based analysis is only for cortical GM. If you mean in GM near > > the CC, then the analysis is appropriate. The projfrac parameter sets > > the sampling location between the white and pial surfaces where 0.5 > > means half way. > > > > On 1/10/17 8:07 AM, John Anderson wrote: > > > > Dear FS experts, > > I am working on surface based analysis using freesurfer. I want to > > inquire about the flag "projfrac" in the command "mris_preproc" > > I ran voxel wise analysis including the same subjects. I found > > differnce between the groups in areas close to the corpus > > callosum. I want to get the same results using surface based > > analysis. If I use the projfrac=0.5 is this able to show the same > > results that I got in voxel wise analysis at the level of the > > corpus callosum. Do I need to use differnt number for projfrac ? > > Thank you for any advice. > > > > Best, > > John > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ Freesurfer mailing > > list Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The > > information in this e-mail is intended only for the person to whom it > > is addressed. If you believe this e-mail was sent to you in error and > > the e-mail contains patient information, please contact the Partners > > Compliance HelpLine at http://www.partners.org/complianceline . If the > > e-mail was sent to you in error but does not contain patient > > information, please contact the sender and properly dispose of the > e-mail. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listi
Re: [Freesurfer] surface based analysis (projfrac)
I am working on surface-based analysis to study the differnce in PET signal in the cortex between two groups. When I used "projfrac=0.5 " there was no differnce between the groups at "cwp 0.05", and when I changed the "projfrac to 0" I got significant differnce between the groups in specific areas at "cwp 0.01". How can I check that this differnce is a real differnce and not related to partial volume effect? Best, John Sent: Friday, January 13, 2017 at 2:46 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis (projfrac) What is the modality you are looking at? On 01/13/2017 02:08 PM, John Anderson wrote: > Thank you very much Doug, > Kindly, do you suggest me any steps to avoid patial volume effects in > surface based analyses ? > Best, > John > *Sent:* Friday, January 13, 2017 at 12:21 PM > *From:* "Douglas N Greve" > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > > > On 01/12/2017 05:20 PM, John Anderson wrote: > > Thank you very much Doug and thank you for briniging the issue of > > "partial volume effect " to my attention. Kindly, I have one last > > question. > > I found in wiki that the default values for projfrc value are between > > 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1, > > 2 ", In other words, less than zero means the surface based analysis > > is running at a lower level of the white matter. > Yes > > Can the issue of the partial volume effect be avoided by using larger > > numbers for "projfrac" ? > No, PVEs can't be avoided that way. > > Bests, > > John > > *Sent:* Thursday, January 12, 2017 at 5:08 PM > > *From:* "Douglas N Greve" > > *To:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > > yes, that is correct. However, understand that there might only be a > > difference of 1mm between those two locations, so it could easily be a > > partial volume effect > > > > > > On 01/11/2017 08:50 AM, John Anderson wrote: > > > Thank you Doug, > > > Exactly! I meant GM near the CC. > > > When I used "projfrac=0.5 " there was no differnce between the groups > > > at "cwp 0.05", and when I changed the "projfrac to 0" I got > > > significant differnce between the groups in specific areas at "cwp > > > 0.01". Kindly, how can this be explained? I highly appreciate if you > > > help me to understand this point: > > > For "projfrac =0" I expect the surface based analysis to > > > be running close to white matter. Right? and when I used > > > "projfrac=0.5" the analysis is running in the middle area between pial > > > and white. When the analysis is not showing any differne between the > > > groups for "projfrac 0.5" and showing differnce for "projfrac 0" that > > > means the differnce between the groups is deeper and closer to white > > > matter. Is this correct? > > > Thank you for any input and clarification! > > > Bests, > > > John > > > *Sent:* Tuesday, January 10, 2017 at 10:51 AM > > > *From:* "Douglas Greve" > > > *To:* freesurfer@nmr.mgh.harvard.edu > > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > > > > > > When you say in the corpus callosum, do you mean in WM? The > > > surface-based analysis is only for cortical GM. If you mean in GM near > > > the CC, then the analysis is appropriate. The projfrac parameter sets > > > the sampling location between the white and pial surfaces where 0.5 > > > means half way. > > > > > > On 1/10/17 8:07 AM, John Anderson wrote: > > > > > > Dear FS experts, > > > I am working on surface based analysis using freesurfer. I want to > > > inquire about the flag "projfrac" in the command "mris_preproc" > > > I ran voxel wise analysis including the same subjects. I found > > > differnce between the groups in areas close to the corpus > > > callosum. I want to get the same results using surface based > > > analysis. If I use the projfrac=0.5 is this able to show the same > > > results that I got in voxel wise analysis at the level of the > > > corpus callosum. Do I need to use differnt number for projfrac ? > > > Thank you for any advice. > > > > > > Best, > > > John > > > >
Re: [Freesurfer] surface based analysis (projfrac)
Thank you Doug for the advice , I will follow your pipeline, I see that the command "gtmseg " is part of Freesurfer 6. Can I apply it on recons generated by Freesurfer 5.3 ? Best, John Sent: Friday, January 13, 2017 at 3:16 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis (projfrac) These differences are hard to track down because they are so subtle. You may want to use our PET module, which includes PVC http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer On 01/13/2017 03:10 PM, John Anderson wrote: > I am working on surface-based analysis to study the differnce in PET > signal in the cortex between two groups. > When I used "projfrac=0.5 " there was no differnce between the groups > at "cwp 0.05", and when I changed the "projfrac to 0" I got > significant differnce between the groups in specific areas at "cwp > 0.01". How can I check that this differnce is a real differnce and > not related to partial volume effect? > Best, > John > *Sent:* Friday, January 13, 2017 at 2:46 PM > *From:* "Douglas N Greve" > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > What is the modality you are looking at? > > > On 01/13/2017 02:08 PM, John Anderson wrote: > > Thank you very much Doug, > > Kindly, do you suggest me any steps to avoid patial volume effects in > > surface based analyses ? > > Best, > > John > > *Sent:* Friday, January 13, 2017 at 12:21 PM > > *From:* "Douglas N Greve" > > *To:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > > > > > > On 01/12/2017 05:20 PM, John Anderson wrote: > > > Thank you very much Doug and thank you for briniging the issue of > > > "partial volume effect " to my attention. Kindly, I have one last > > > question. > > > I found in wiki that the default values for projfrc value are between > > > 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1, > > > 2 ", In other words, less than zero means the surface based analysis > > > is running at a lower level of the white matter. > > Yes > > > Can the issue of the partial volume effect be avoided by using larger > > > numbers for "projfrac" ? > > No, PVEs can't be avoided that way. > > > Bests, > > > John > > > *Sent:* Thursday, January 12, 2017 at 5:08 PM > > > *From:* "Douglas N Greve" > > > *To:* freesurfer@nmr.mgh.harvard.edu > > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > > > yes, that is correct. However, understand that there might only be a > > > difference of 1mm between those two locations, so it could easily be a > > > partial volume effect > > > > > > > > > On 01/11/2017 08:50 AM, John Anderson wrote: > > > > Thank you Doug, > > > > Exactly! I meant GM near the CC. > > > > When I used "projfrac=0.5 " there was no differnce between the > groups > > > > at "cwp 0.05", and when I changed the "projfrac to 0" I got > > > > significant differnce between the groups in specific areas at "cwp > > > > 0.01". Kindly, how can this be explained? I highly appreciate if you > > > > help me to understand this point: > > > > For "projfrac =0" I expect the surface based analysis to > > > > be running close to white matter. Right? and when I used > > > > "projfrac=0.5" the analysis is running in the middle area > between pial > > > > and white. When the analysis is not showing any differne between the > > > > groups for "projfrac 0.5" and showing differnce for "projfrac 0" > that > > > > means the differnce between the groups is deeper and closer to white > > > > matter. Is this correct? > > > > Thank you for any input and clarification! > > > > Bests, > > > > John > > > > *Sent:* Tuesday, January 10, 2017 at 10:51 AM > > > > *From:* "Douglas Greve" > > > > *To:* freesurfer@nmr.mgh.harvard.edu > > > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > > > > > > > > When you say in the corpus callosum, do you mean in WM? The > > > > surface-based analysis is only for cortical GM. If you mean in > GM near > > > > the CC, then the analysis is appropriate. The pro
[Freesurfer] Tracula Tracts density
Hi Anastasia, How can I calculate the tract density from the output of tracula. For example in the final stats file for the cortico spinal tract I can see the number of sample paths in the WM tract. Is this number refer to the tract density ( number of DTI fibers comprising the tract - in other words the number of distinct tracts that pass through the manually constructed sets of ROIs) ? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all stripped brains
Dear experts, I want to run recon-all on a stripped brains ( T1 images after applying bet tool). Do I need to add any flags to the command recon -all -all subjid Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] MPRAGE SNR
Dear Experts, Is there any tool in Freesurfer that can help to evaluate the SNR for T1 MPRAGE images directly ( i.e script). If not knidly can any help me to figure out the best way to dao it. I highly appreciate your help! Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] MPRAGE SNR
Dear Jürgen This really helps! I highly appreciate your input on this. Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, October 19, 2015 at 1:30 AM From: JuergenHaenggi To: "Freesurfer support list" Subject: Re: [Freesurfer] MPRAGE SNR Dear John FS's QA tools provide the SNR see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools there is also a FS function called wm-anat-snr that can be used for that. Hope this helps Cheers Jürgen - Jürgen Hänggi, Ph.D. Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haen...@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. - Am 18.10.2015 um 16:48 schrieb John Anderson: Dear Experts, Is there any tool in Freesurfer that can help to evaluate the SNR for T1 MPRAGE images directly ( i.e script). If not knidly can any help me to figure out the best way to dao it. I highly appreciate your help! Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] MPRAGE SNR
Hi Bruce, Thanks a lot!! this is really great! I ran the command as the following : mri_cnr subj_01/surf subj_01/mri/norm.mgz processing MRI volume subj_01/mri/norm.mgz... white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5 gray/white CNR = 2.291, gray/csf CNR = 0.848 lh CNR = 1.569 white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0 gray/white CNR = 2.278, gray/csf CNR = 0.798 rh CNR = 1.538 total CNR = 1.554 I noticed that the normal range for the SNR (15-20) when using the command "wm-anat-snr" What is the normal range for cnr generated by the binary "mri_cnr"? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, October 19, 2015 at 8:36 AM From: "Bruce Fischl" To: "Freesurfer support list" Cc: j.haen...@psychologie.uzh.ch Subject: Re: [Freesurfer] MPRAGE SNR Hi John there is also a binary called mri_cnr that will compute the contrast-to-noise ratio (CNR), which is really the more interesting metric. It will also spit out the WM means+- std, and the ratio of these two can be used as an SNR measure. cheers Bruce On Mon, 19 Oct 2015, John Anderson wrote: > Dear Jürgen > This really helps! > I highly appreciate your input on this. > > Bests, > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > Sent: Monday, October 19, 2015 at 1:30 AM > From: JuergenHaenggi > To: "Freesurfer support list" > Subject: Re: [Freesurfer] MPRAGE SNR > Dear John > FS's QA tools provide the SNR > see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools > > there is also a FS function called wm-anat-snr that can be used for that. > > Hope this helps > Cheers > Jürgen > > --- > -- > Jürgen Hänggi, Ph.D. > Division of Neuropsychology > Institute of Psychology > University of Zurich > Binzmuehlestrasse 14, PO Box 25 > 8050 Zurich, Switzerland > 0041 44 635 73 97 (phone office) > 0041 76 445 86 84 (phone mobile) > 0041 44 635 74 09 (fax office) > BIN 4.D.04 (office room number) > j.haen...@psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > > This e-mail (and any attachment/s) contains confidential and/or privileged > information. If you are not the intended recipient (or have received this > e-mail in error) please notify the sender immediately and destroy this > e-mail. Any unauthorised copying, disclosure or distribution of the > material in this e-mail is strictly forbidden. > --- > -- > > > > Am 18.10.2015 um 16:48 schrieb John Anderson: > > Dear Experts, > Is there any tool in Freesurfer that can help to evaluate the SNR for > T1 MPRAGE images directly ( i.e script). If not knidly can any help me > to figure out the best way to dao it. > > I highly appreciate your help! > > Bests, > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > ___ Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information > in this e-mail is intended only for the person to whom it is addressed. If > you believe this e-mail was sent to you in error and the e-mail contains > patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error but does no
Re: [Freesurfer] MPRAGE SNR
Hi All, Thank you very much for your comments! Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness? Does it make sence ? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, October 19, 2015 at 11:48 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MPRAGE SNR This has been my experience as well. Not much seems to predict which scans will need to be edited. On 10/19/15 10:23 AM, Harms, Michael wrote: > Hi, > > FWIW, I've looked at a number of these measures in 500+ subjects from HCP > data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they > relate to each other, and whether they correlate with mean cortical > thickness, white matter surface area, or number of SurfaceHoles (prior to > topology correction). > > I didn't find much of note. e.g., the highest correlations were: > > r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz) > r = -0.25 between white surface area and wmanatsnr > r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from > norm.mgz) > > Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r = > 0.49). > > G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80. > G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97 > > In another context (but smaller number of subjects), I've looked to see if > these various snr, cnr measures from FS were related to manual quality > ratings, and the relationship was rather weak. > > All-in-all, I haven't seen much that would indicate that these measures > can be used as a sort of "automated" QC measure. Manual review of the > structurals and FS results is still needed. > > That said, the structurals from the HCP 500 release were all of reasonably > good quality to begin with. So, it is possible that these snr/cnr > measures might be more informative in identifying truly awful scans in a > clinical population with a wider variability in MPRAGE scan quality. > > I'd certainly be interested in hearing from anyone if they have found that > to be the case in their data. > > BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from > orig.mgz and norm.mgz respectively. > Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave.Tel: 314-747-6173 > St. Louis, MO 63110Email: mha...@wustl.edu > > > > > On 10/19/15 8:09 AM, "Bruce Fischl" wrote: > > probably similar, although maybe Doug can comment. You probably want to > run > it on the orig.mgz as the intensity normalization can artificially > increase > the SNR (which is kind of the point) > Bruce > > > On Mon, 19 Oct 2015, John > Anderson wrote: > >> Hi Bruce, >> Thanks a lot!! this is really great! >> I ran the command as the following : >> >> mri_cnr subj_01/surf subj_01/mri/norm.mgz >> processing MRI volume subj_01/mri/norm.mgz... >> white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5 >> gray/white CNR = 2.291, gray/csf CNR = 0.848 >> lh CNR = 1.569 >> white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0 >> gray/white CNR = 2.278, gray/csf CNR = 0.798 >> rh CNR = 1.538 >> total CNR = 1.554 >> >> >> I noticed that the normal range for the SNR (15-20) when using the >> command >> "wm-anat-snr" >> >> What is the normal range for cnr generated by the binary "mri_cnr"? >> >> >> Bests, >> John Anderson >> >> Senior Research Associate >> Psychological and Brain Sciences Dept. >> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 >> Phone: +1 (603) 646-9834 >> Fax: +1 (603) 646-1419 >> Sent: Monday, October 19, 2015 at 8:36 AM >> From: "Bruce Fischl" >> To: "Freesurfer support list" >> Cc: j.haen...@psychologie.uzh.ch >> Subject: Re: [Freesurfer] MPRAGE SNR >> Hi John >> >> there is also a binary called mri_cnr that will compute the >> contrast-to-noise ratio (CNR), which is really the more interesting >> metric. It will also spit out the WM means+- std, and the ratio of th
Re: [Freesurfer] MPRAGE SNR
Thanks MH, Let's say that we have 100 MPRAGEs and we want to include them in a cross sectional analysis. Depending on your experience, do you recommend any criterion to (include/ exclude) these images in the analysis? As I see visualizing the images alone is not enough to say that the quality of the image is fine. Also calculating the SNR, CNR want help a lot! any suggestions? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, October 19, 2015 at 12:24 PM From: "Harms, Michael" To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] MPRAGE SNR At best that would probably be harmless (if you have a decent number of subjects), but unless SNR, CNR actually relates to those measures in some fashion, you aren't really accomplishing anything by including it as a covariate. You certainly wouldn't be able to claim that including SNR as a covariate has somehow "controlled" for MPRAGE data quality because there doesn't appear to be much of a relationship in the first place. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: John Anderson <j.ander...@publicist.com> Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Date: Monday, October 19, 2015 10:57 AM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] MPRAGE SNR Hi All, Thank you very much for your comments! Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness? Does it make sence ? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Monday, October 19, 2015 at 11:48 AM From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MPRAGE SNR This has been my experience as well. Not much seems to predict which scans will need to be edited. On 10/19/15 10:23 AM, Harms, Michael wrote: > Hi, > > FWIW, I've looked at a number of these measures in 500+ subjects from HCP > data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they > relate to each other, and whether they correlate with mean cortical > thickness, white matter surface area, or number of SurfaceHoles (prior to > topology correction). > > I didn't find much of note. e.g., the highest correlations were: > > r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz) > r = -0.25 between white surface area and wmanatsnr > r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from > norm.mgz) > > Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r = > 0.49). > > G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80. > G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97 > > In another context (but smaller number of subjects), I've looked to see if > these various snr, cnr measures from FS were related to manual quality > ratings, and the relationship was rather weak. > > All-in-all, I haven't seen much that would indicate that these measures > can be used as a sort of "automated" QC measure. Manual review of the > structurals and FS results is still needed. > > That said, the structurals from the HCP 500 release were all of reasonably > good quality to begin with. So, it is possible that these snr/cnr > measures might be more informative in identifying truly awful scans in a > clinical population with a wider variability in MPRAGE scan quality. > > I'd certainly be interested in hearing from anyone if they have found that > to be the case in their data. > > BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from > orig.mgz and norm.mgz respectively. > Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid
[Freesurfer] Head circumference
Dear FS experts, I want to inquire if there is any script in Freesurfer that can help to calculate the head circumference from MPRAGE ? Thanks for any advice! Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Head circumference
Dear FS experts, I want to inquire if there is any tool or method in Freesurfer that can help to calculate the head circumference from MPRAGE ? Thanks for any advice! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Voxel based vs surface based
Hi Doug and Bruce, Kindly, I have question regarding the difference between voxel based ( VBM/ FSL pipeline) and surface based analysis ( Freesurfer ). I have two groups of subjects Group A and Group B I ran morphometric analysis in Freesurfer ( recon-all then manual edits) to check the difference in cortical thickness between the groups. Then I used Qdec to correct the results for multiple comparisons and to visualize the significant clusters. Then I ran VBM analysis between the groups ( the same subjects) to study the difference in gray matter volume between the groups. I got significant difference between the groups in both methods but in different areas of the brain ( the significant clusters are not in the same location ). What is the difference between surface based analysis and voxel based analysis technically. Is it right to get different results? Thanks in advance Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all
Hi freesurfers, Following recon-all I have a collection of folders inside the subject folder. Inside the folder "mri" I have collection of files: 1. What is the differnce between the file "orig.mgz" and the file "norm.mgz" ? 2. Why the voxel dimentions are differnt? (i.e In norm.mgz the voxel dimentions are equal while in orig.mgz it is not)? 3. Is it correct if I convert norm.mgz to "nii" file and use it as a "T1" for further processing? bests, John Anderson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all
Thanks a lot Doug! Kindly ... 1. What do you mean by intensity normalized? 2. What is the purpose of conforming the inputs to 256^3 1mm3 3. In order to move mask to diffusion space (FA map) or PET space I do the following: 3.1 I register FA map to T1 ( after converting the DICOMs to T1.nii - the voxel dimentions here are 176X256X256) 3.2 I create mask of interest using mri_binarize ( from the wmparc.mgz atals the voxel dimentions here 256X256X256 ) 3.3 I register FA map to T1 image using FLIRT 3.4 I register the mask to T1 using FLIRT 3.5 I use reversed matrix to move the mask to FA map. The problem in this approach is the voxel dimentions ( between the mask and the T1). Can I use norm.mgz ( which has the same voxel dimentions of the mask ) istead of T1 to do the previous steps? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Wednesday, November 04, 2015 at 3:44 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all On 11/04/2015 10:22 AM, John Anderson wrote: > Hi freesurfers, > Following recon-all I have a collection of folders inside the subject > folder. > Inside the folder "mri" I have collection of files: > 1. What is the differnce between the file "orig.mgz" and the file > "norm.mgz" ? norm has been skull stripped and intensity normalized > 2. Why the voxel dimentions are differnt? (i.e In norm.mgz the voxel > dimentions are equal while in orig.mgz it is not)? They should be the same. It might be differnt than rawavg.mgz or your input data because we "conform" all inputs to 256^3 1mm3 > 3. Is it correct if I convert norm.mgz to "nii" file and use it as a > "T1" for further processing? I don't know without knowing more about the "further processing". It is not a T1 image itself (ie, the voxel intensities are not T1 in msec). > bests, > John Anderson > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all
Hi Doug, Thanks you very much for your great and detailed answered. Kindly one more thing: when I am tring to run recon-all on "001.mgz" (under the folder mri/orig). If the fov is more than 256 ( e.g 320) recon-all failed. I checked the "recon-all.log" file and I found that it failed because the fov is more than 320 and it says that I need to run recon -all with the flag -cw256. How can the fov affect the segmentation? in other words is it better to run recon-all on a file with fov less than 256 or more than 256 ? what is the difference in the final output? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Thursday, November 05, 2015 at 9:39 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all On 11/5/15 8:37 AM, John Anderson wrote: Thanks a lot Doug! Kindly ... 1. What do you mean by intensity normalized? Removing non-biological intensity fluctuations such as darkening/brightening from multiple head coils 2. What is the purpose of conforming the inputs to 256^3 1mm3 This is something that was done when FS was first programmed to make it easier to program by assuring that all inputs were the same size. 3. In order to move mask to diffusion space (FA map) or PET space I do the following: 3.1 I register FA map to T1 ( after converting the DICOMs to T1.nii - the voxel dimentions here are 176X256X256) 3.2 I create mask of interest using mri_binarize ( from the wmparc.mgz atals the voxel dimentions here 256X256X256 ) 3.3 I register FA map to T1 image using FLIRT 3.4 I register the mask to T1 using FLIRT 3.5 I use reversed matrix to move the mask to FA map. Probably works, but very compilcated. You should use bbregister to register the FA or PET directly to the conformed space, then use mri_label2vol to map the mask into FA/PET space. The problem in this approach is the voxel dimentions ( between the mask and the T1). Can I use norm.mgz ( which has the same voxel dimentions of the mask ) istead of T1 to do the previous steps? Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 Sent: Wednesday, November 04, 2015 at 3:44 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all On 11/04/2015 10:22 AM, John Anderson wrote: > Hi freesurfers, > Following recon-all I have a collection of folders inside the subject > folder. > Inside the folder "mri" I have collection of files: > 1. What is the differnce between the file "orig.mgz" and the file > "norm.mgz" ? norm has been skull stripped and intensity normalized > 2. Why the voxel dimentions are differnt? (i.e In norm.mgz the voxel > dimentions are equal while in orig.mgz it is not)? They should be the same. It might be differnt than rawavg.mgz or your input data because we "conform" all inputs to 256^3 1mm3 > 3. Is it correct if I convert norm.mgz to "nii" file and use it as a > "T1" for further processing? I don't know without knowing more about the "further processing". It is not a T1 image itself (ie, the voxel intensities are not T1 in msec). > bests, > John Anderson > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___
Re: [Freesurfer] Qdec visualization
Thanks you very much Doug, Please one more question. Is there any way in Qdec to get the stamdard error (SE) ? Bests, John Sent: Monday, December 21, 2015 at 11:43 AM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec visualization The correction for multiple comparisons is cluster-based. Each cluster gets a single number. In the display, all the vertices get that same number. On 12/18/2015 03:17 PM, John Anderson wrote: > Hi Freesurfer experts, > I am using Qdec in Freesurfer 5.3 to do some cortical thickness > comparisons between two groups. > > Before corrcting the results for multiple comparisons ( monte carlo > simulation) the significant differnce between the groups is visualized > as a range of color while after correcting for multiple copmparisons > the color of the statistical map is usinform ( Attached) > Is ther any way to visualze the results as a range of color after > correcting the results for multiple comparsiosn > > Thanks in advance for any advice > Bests, > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Qdec visualization
Hi Doug, Given that the standard variance can be calculated using the command "mris_calc" and the flag "-sqrt" what is the correct command to do this calculation? I tried: mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly what I am doing wrong? Bests, John Sent: Monday, December 21, 2015 at 2:20 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec visualization QDEC cannot but the information may be in the output folder. There should be a file called gammavar.mgh. This will be the standard variance (so take the square root) On 12/21/2015 02:08 PM, John Anderson wrote: > Thanks you very much Doug, > Please one more question. Is there any way in Qdec to get the stamdard > error (SE) ? > Bests, > John > *Sent:* Monday, December 21, 2015 at 11:43 AM > *From:* "Douglas N Greve" > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Qdec visualization > The correction for multiple comparisons is cluster-based. Each cluster > gets a single number. In the display, all the vertices get that same > number. > > On 12/18/2015 03:17 PM, John Anderson wrote: > > Hi Freesurfer experts, > > I am using Qdec in Freesurfer 5.3 to do some cortical thickness > > comparisons between two groups. > > > > Before corrcting the results for multiple comparisons ( monte carlo > > simulation) the significant differnce between the groups is visualized > > as a range of color while after correcting for multiple copmparisons > > the color of the statistical map is usinform ( Attached) > > Is ther any way to visualze the results as a range of color after > > correcting the results for multiple comparsiosn > > > > Thanks in advance for any advice > > Bests, > > John Anderson > > > > Senior Research Associate > > Psychological and Brain Sciences Dept. > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > > Phone: +1 (603) 646-9834 > > Fax: +1 (603) 646-1419 > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Qdec visualization
Thanks Doug, I used the command "mris_calc gammavar.mgh sqrt" and the output was: "Saving result to 'out.mgz' (type = MGH )" Then I ran the command "mris_calc out.mgz stats" and the output was : Size [ 163842 ] Min@(index) [ 0.00 (161385) ] Max@(index) [ 0.259395 (18208) ] Mean [ 0.097956 ] Std [ 0.040943 ] Sum [ 16049.365234 ] Prod [ 0.00 ] In order to calculate the standard error is it fine if I use mris_calc gammavar.mgh stats the I divide the Std of gammavar.mgh by the square root of the sample size ( number of subjects included in the analysis)? Thanks a lot! Sent: Monday, December 21, 2015 at 2:44 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec visualization it helps to see the error msg, but my guess is that you need to specify an mgh file, not a txt file. This will give you the voxel-wise stderr, not a standard error for the cluster (which does not make sense) On 12/21/2015 02:38 PM, John Anderson wrote: > Hi Doug, > Given that the standard variance can be calculated using the command > "mris_calc" and the flag "-sqrt" what is the correct command to do > this calculation? > I tried: > mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly > what I am doing wrong? > Bests, > John > *Sent:* Monday, December 21, 2015 at 2:20 PM > *From:* "Douglas N Greve" > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Qdec visualization > QDEC cannot but the information may be in the output folder. There > should be a file called gammavar.mgh. This will be the standard variance > (so take the square root) > > On 12/21/2015 02:08 PM, John Anderson wrote: > > Thanks you very much Doug, > > Please one more question. Is there any way in Qdec to get the stamdard > > error (SE) ? > > Bests, > > John > > *Sent:* Monday, December 21, 2015 at 11:43 AM > > *From:* "Douglas N Greve" > > *To:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] Qdec visualization > > The correction for multiple comparisons is cluster-based. Each cluster > > gets a single number. In the display, all the vertices get that same > > number. > > > > On 12/18/2015 03:17 PM, John Anderson wrote: > > > Hi Freesurfer experts, > > > I am using Qdec in Freesurfer 5.3 to do some cortical thickness > > > comparisons between two groups. > > > > > > Before corrcting the results for multiple comparisons ( monte carlo > > > simulation) the significant differnce between the groups is visualized > > > as a range of color while after correcting for multiple copmparisons > > > the color of the statistical map is usinform ( Attached) > > > Is ther any way to visualze the results as a range of color after > > > correcting the results for multiple comparsiosn > > > > > > Thanks in advance for any advice > > > Bests, > > > John Anderson > > > > > > Senior Research Associate > > > Psychological and Brain Sciences Dept. > > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > > > Phone: +1 (603) 646-9834 > > > Fax: +1 (603) 646-1419 > > > > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom > > it is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact t
[Freesurfer] Longitudinal data analysis
Hi Martin, I am working on a logitudinal data analysis using freesurfer pipeline. I followed all the steps like in WIKI and the analysis was great. Kindly I have the following questions: 1. In wiki "http://freesurfer.net/fswiki/LinearMixedEffectsModels"-- in the example mentioned there, the command " lme_lowessPlot(M(:,1),Y(:,1)+Y(:,2),0.70,M(:,2));" What is the Y(:,2) refer to ? 2. Can I plot multiple measures at the same time ( for example if I have in my qdec table multiple columns for multiple measures ( left precentral gyrus cortical thickness, right precentral gyrus cortical thickness, LH mean thickness , RH mean thickness) can I plot all these measures at the same time instead of running the previous command multiple times? 3. The BW in this command was chosen 0.7 and the default is 0.6 how can I choose this number correctly? Tanks for your support! Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Longitudinal data analysis
Hi Freesurfer experts, I am working on a logitudinal data analysis using freesurfer pipeline. I followed all the steps like in WIKI and the analysis was great. Kindly I have the following questions: 1. In wiki "http://freesurfer.net/fswiki/LinearMixedEffectsModels"-- in the example mentioned there, the command " lme_lowessPlot(M(:,1),Y(:,1)+Y(:,2),0.70,M(:,2));" What is the Y(:,2) refer to ? 2. Can I plot multiple measures at the same time ( for example if I have in my qdec table multiple columns for multiple measures ( left precentral gyrus cortical thickness, right precentral gyrus cortical thickness, LH mean thickness , RH mean thickness) can I plot all these measures at the same time instead of running the previous command multiple times? 3. If I have three groups in my qdec table. The previous command line is plotting three lines. Are these lines in th esame order of the groups in qdec tables? 4. The BW in this command was chosen 0.7 and the default is 0.6 how can I choose this number correctly? Thanks for your support! Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] P files
Dear Freesurfer experts, I want to inquire if there is any tool in Freesurfer that can help to convert the p files ( raw data generated by GE scanner ) to DICOMs Thanks for any advice! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] transform statistical map in MNI to surface
Hi Experts, I have statistical map in MNI space and I want to view it using tksurfer how can i transform this map to a surface ? Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] transform statistical map in MNI to surface
Thanks you Doug, Kindly how can I run recon-all on the statistical map ? my statistical map is an output of TBSS analysis Bests, John Sent: Friday, January 08, 2016 at 1:41 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] transform statistical map in MNI to surface If it is in mni152 space, then you can run recon-all on the mni152 T1 map, then use mri_vol2surf with --regheader to map the volume tothe surface, then use tksurfer or freeview to view the resulting map On 01/08/2016 12:49 PM, John Anderson wrote: > Hi Experts, > I have statistical map in MNI space and I want to view it using > tksurfer how can i transform this map to a surface ? > > Bests, > John > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] transform statistical map in MNI to surface
Thanks Bruce, if my statistical map "stat1.nii.gz" is in MNI152 standard space what are the command lines that I need ( or if possible any link to wiki) Thanks a lot! John Sent: Friday, January 08, 2016 at 2:49 PM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] transform statistical map in MNI to surface you wouldn't run it on the stats map - you would run it on the T1-weighted MNI152 volume On Fri, 8 Jan 2016, John Anderson wrote: > Thanks you Doug, > Kindly how can I run recon-all on the statistical map ? my statistical map > is an output of TBSS analysis > > Bests, > John > Sent: Friday, January 08, 2016 at 1:41 PM > From: "Douglas N Greve" > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] transform statistical map in MNI to surface > If it is in mni152 space, then you can run recon-all on the mni152 T1 > map, then use mri_vol2surf with --regheader to map the volume tothe > surface, then use tksurfer or freeview to view the resulting map > > On 01/08/2016 12:49 PM, John Anderson wrote: > > Hi Experts, > > I have statistical map in MNI space and I want to view it using > > tksurfer how can i transform this map to a surface ? > > > > Bests, > > John > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Cortical thickness parcellates
Dear experts, I am wondering if there is any way to divide the cortical thickness parcellates in the atlas "?h.aparc.annot" by lobe. I highly appreciate any suggestion. Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical thickness parcellates
Thanks Doug, I aim to create masks for the frontal lobe , parietal lobe, occipital lobe and temporal lobe including all the parcellates in every lobe in one maks. I was thinking to use mri_binarize but the number of the parcellates is very big. Is there a way that can give a direct maks for cortical thickness by lobe? Sent: Wednesday, January 13, 2016 at 12:41 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cortical thickness parcellates Try mris_divide_parcellation On 01/13/2016 12:18 PM, John Anderson wrote: > Dear experts, > I am wondering if there is any way to divide the cortical thickness > parcellates in the atlas "?h.aparc.annot" by lobe. I highly appreciate > any suggestion. > > Bests, > John > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Longitudinal analysis_covariates
Dear Dr Martin, I have longitudinal database for subjects scanned multiple times. I want to study the changes in cortical thickness over time. I prepared my longitudinal table ( column#1 fsid column#2 fsid-base column#3 group column#4 bilateral motor cortex thickness column#5 time (years) column#6 disease duration) Then I followed the instructions like in wiki... and I plot the changes in motor cortex over time using the command : lme_lowessPlot(M:,5),Y(:,1)m0.7,M(:,3)) My questions are: 1. How can I regress the effect of disease duration (column#6) ? is it by running the previous command line by replaceing M(:,5) ( time) by M(:,6) disease duration? 2. If I am interested in studying the change in cortical thickness by the change in clinical scale over time is it correct to replce the coloumn #5 ( time) by a column for the clinical scales? Thanks in advance for any advice! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] register image to mni152
Dear experts, I wanted to register T1 mprage image to the standard space MNI152. The output of FLIRT at dof 12 is not effective. How can I get better results using bbregister? What are the commands that I need to use ? thanks for any help! John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] transform statistical map in MNI to surface
Hi Bruce, I carefully followed your orientations. Kindly I still need more clarification regarding the following point: I have statistical map in MNI152 space (volume) as an output of permutation analysis using " randomise/FSL". I want to visualize this map on an inflated surface in Freesurfer. 1. Can I directly use the command " tksurfer fsaverage rh inflated -overlay-reg $FREESURFER_HOME/average/mni152.register.dat -o "my tstat map" 2. Whay I need to do segmentation to MNI152 then running the command mri_vol2surf? Whar are the cons and pros of doing or not doing these steps? Thanks a lot! John Sent: Friday, January 08, 2016 at 2:57 PM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] transform statistical map in MNI to surface Hi John you would run recon-all on the MNI 152 T1 image (NOT your map), then use mri_vol2surf to map the stats map onto the resulting surfaces. Note that this won't give you great results as a bunch of your clusters will probably not be near the cortical surface (since in general subjects cortices don't align well in MNI 152) cheers Bruce On Fri, 8 Jan 2016, John Anderson wrote: > Thanks Bruce, > if my statistical map "stat1.nii.gz" is in MNI152 standard space what are > the command lines that I need ( or if possible any link to wiki) > Thanks a lot! > > > John > Sent: Friday, January 08, 2016 at 2:49 PM > From: "Bruce Fischl" > To: "Freesurfer support list" > Subject: Re: [Freesurfer] transform statistical map in MNI to surface > you wouldn't run it on the stats map - you would run it on the > T1-weighted MNI152 volume > > > Sent: Friday, January 08, 2016 at 1:41 PM > > From: "Douglas N Greve" > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] transform statistical map in MNI to surface > > If it is in mni152 space, then you can run recon-all on the mni152 T1 > > map, then use mri_vol2surf with --regheader to map the volume tothe > > surface, then use tksurfer or freeview to view the resulting map > > > > On 01/08/2016 12:49 PM, John Anderson wrote: > > > Hi Experts, > > > I have statistical map in MNI space and I want to view it using > > > tksurfer how can i transform this map to a surface ? > > > > > > Bests, > > > John > > > > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom it > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail
[Freesurfer] Longitudinal analysis--mass univariate
Hi Dr Martin, I have two groups of patients and one group of controls. The patients scanned multiple times but the number of time points is different between the subjects. The controls have only one time point. I aim to : 1. I wanted to study the changes in cortical thickness over time in each group of patients. 2. I wanted to compare the change in cortical thickness between patients and controls over time. I followed wiki and I choose LME to run the analysis. My questions are: 1. Can I use mass univariate analysis to check the changes in cortical thickness over time in only one group of patients. The example In wiki was for four groups. 2. Can I do a comparison in cortical thickness over time between controls ( who have only one time point ) and patients using mass univariate approach. Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal analysis--mass univariate
Thanks a lot D martin for your quick answer. Regarding my patients I have two groups but the subject in every group have differnt time points. i.e Group-patients 1: I have 100 patients some scanned three times and some four times the rest at least two times. Group-Patients 2: is consisted of 75 patients some also some scanned three times and some four times the rest at least two times. Is LME -- mas usnivariate still workable with out a bias ? Bests, John Sent: Thursday, January 28, 2016 at 6:51 AM From: "Martin Reuter" To: "Freesurfer support list" Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate Hi John, you should check if the number of time points per subject is relatively random across your two patient groups. You don’t want a bias, let’s say one patient group with 2 tp and the other with 3. You can compare the atrophy across these two groups easily with LME. Or you can also test if the rate is different from zero in each individual group. You will never be able to compute atrophy rates for your control group (as you only have a single time point for them) so you cannot compare with them either. Best, Martin On Jan 28, 2016, at 12:23 PM, John Anderson <j.ander...@publicist.com> wrote: Hi Dr Martin, I have two groups of patients and one group of controls. The patients scanned multiple times but the number of time points is different between the subjects. The controls have only one time point. I aim to : 1. I wanted to study the changes in cortical thickness over time in each group of patients. 2. I wanted to compare the change in cortical thickness between patients and controls over time. I followed wiki and I choose LME to run the analysis. My questions are: 1. Can I use mass univariate analysis to check the changes in cortical thickness over time in only one group of patients. The example In wiki was for four groups. 2. Can I do a comparison in cortical thickness over time between controls ( who have only one time point ) and patients using mass univariate approach. Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal analysis--mass univariate {Disarmed}
Dear Dr Martin ,
Thanks a lot for your kindness and your great answers!!
Please I have one more question regarding the design matrix:
If I use my design matrix for LME depending on the exampels mentioned in FS wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Is this correct?
Bests,
John
Sent: Saturday, January 30, 2016 at 5:51 AM
From: "Martin Reuter"
To: "Freesurfer support list"
Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate {Disarmed}
Hi John,
What I mean is there could be a bias in your study design if 99% of group 1 have three or more time points and 99% of group 2 have only two time points. This is something you should check. If distributions are approximately similar, you’d be fine. LME can be used in either case. If there is any biases (also age, gender etc) you’d probably want to control for it via additional co-variates in your LME model.
Best, Martin
On Jan 28, 2016, at 1:12 PM, John Anderson <j.ander...@publicist.com> wrote:
Thanks a lot D martin for your quick answer.
Regarding my patients I have two groups but the subject in every group have differnt time points. i.e Group-patients 1: I have 100 patients some scanned three times and some four times the rest at least two times.
Group-Patients 2: is consisted of 75 patients some also some scanned three times and some four times the rest at least two times.
Is LME -- mas usnivariate still workable with out a bias ?
Bests,
John
Sent: Thursday, January 28, 2016 at 6:51 AM
From: "Martin Reuter" <mreu...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate
Hi John,
you should check if the number of time points per subject is relatively random across your two patient groups. You don’t want a bias, let’s say one patient group with 2 tp and the other with 3.
You can compare the atrophy across these two groups easily with LME. Or you can also test if the rate is different from zero in each individual group.
You will never be able to compute atrophy rates for your control group (as you only have a single time point for them) so you cannot compare with them either.
Best, Martin
On Jan 28, 2016, at 12:23 PM, John Anderson <MailScanner has detected a possible fraud attempt from "x-msg:" claiming to be j.ander...@publicist.com> wrote:
Hi Dr Martin,
I have two groups of patients and one group of controls.
The patients scanned multiple times but the number of time points is different between the subjects.
The controls have only one time point.
I aim to :
1. I wanted to study the changes in cortical thickness over time in each group of patients.
2. I wanted to compare the change in cortical thickness between patients and controls over time.
I followed wiki and I choose LME to run the analysis.
My questions are:
1. Can I use mass univariate analysis to check the changes in cortical thickness over time in only one group of patients. The example In wiki was for four groups.
2. Can I do a comparison in cortical thickness over time between controls ( who have only one time point ) and patients using mass univariate approach.
Bests,
John
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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[Freesurfer] Qdec-statistical map
Dear FS experts, I am using Qdec to study the differnce in cortical thicnkess between two groups. Qdec is running a GLM analysis. This will output a statistical map (sig.mgh) for the differnce between the groups in cortical thicnkess. How can I extract the numbers of cortical thickness for every subject (depending on the order of subjects in Qdec table) from this statistical map ? Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Qdec-statistical map
Hi Doug, How can I use this statistical map ( e.g. as a mask) to calculate the mean cortical thickness only in the areas of significant differnce between the groups for every subject? Bests, John Sent: Thursday, March 03, 2016 at 12:37 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec-statistical map not sure what you mean. the statistical map will have a single value, not a value for each subject On 03/03/2016 12:31 PM, John Anderson wrote: > Dear FS experts, > I am using Qdec to study the differnce in cortical thicnkess between > two groups. > Qdec is running a GLM analysis. This will output a statistical map > (sig.mgh) for the differnce between the groups in cortical thicnkess. > How can I extract the numbers of cortical thickness for every > subject (depending on the order of subjects in Qdec table) from this > statistical map ? > Bests, > John > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Qdec-statistical map
This si Great!!! Thanks Doug. One more question: What is the correct input in the command mri_surfcluster. Is it the image "sig.mgh" ? Bests, John Sent: Thursday, March 03, 2016 at 12:47 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec-statistical map You will have to extract clusters (mri_surfcluster) to create an annotation, then use mri_segstats with the --annot option and specifying the y.mgh file as input and the output using something like --avgwf output.txt (also add --exludeid 0). The output will have a row for each frame in y.mgh (ie, each subject) and a column for each cluster On 03/03/2016 12:43 PM, John Anderson wrote: > Hi Doug, > How can I use this statistical map ( e.g. as a mask) to calculate the > mean cortical thickness only in the areas of significant differnce > between the groups for every subject? > Bests, > John > *Sent:* Thursday, March 03, 2016 at 12:37 PM > *From:* "Douglas N Greve" > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Qdec-statistical map > not sure what you mean. the statistical map will have a single value, > not a value for each subject > > On 03/03/2016 12:31 PM, John Anderson wrote: > > Dear FS experts, > > I am using Qdec to study the differnce in cortical thicnkess between > > two groups. > > Qdec is running a GLM analysis. This will output a statistical map > > (sig.mgh) for the differnce between the groups in cortical thicnkess. > > How can I extract the numbers of cortical thickness for every > > subject (depending on the order of subjects in Qdec table) from this > > statistical map ? > > Bests, > > John > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_glmfit
Hi FS experts, I am trying to run OSGM analysis between two groups using mri_glmfit as follow : mri_glmfit --y lh_10mm.mgh --fsgd fsgd.dat --glmdir lh_10mm --surf fsaverage lh --osgm it keep returning as: ERROR: DOF = 0 my FSGD is as follow GroupDescriptorFile 1 Title OSGM Class group1 Class group2 Input 001 group1 Input 002 group1 Input 003 group1 Input 004 group1 . . . Input C001 group2 Input C002 group2 Input C003 group2 Input C004 group2 . . . please what I am doing wrong?! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FA maps surface based analysis
Hi FS experts, How can ai do surface based analysis on FA maps. In other wods: I have 20 subjects( two groups 10/10) and FA map for every subject. How can I dtufy the differnce between the groups in FA on surface? Best, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_glmfit-sim
Hi experts, I am trying to correct the results of groups analysis using mri_glmfit-sim the command is : mri_glmfit-sim --glmdir lh_10mm --cache 3 pos --cwpvalthresh .0166 I receive the follwoing error : ERROR: cannot find /usr/local/freesurfer/stable6/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/pos/th30/mc-z.csd Thanks you for any suggestion! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fw: mri_glmfit-sim
Hi FS experts, I am trying to correct the results of groups analysis using mri_glmfit-sim the command is : mri_glmfit-sim --glmdir lh_10mm --cache 3 pos --cwpvalthresh .0166 I receive the follwoing error : ERROR: cannot find /usr/local/freesurfer/stable6/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/pos/th30/mc-z.csd Thanks you for any suggestion! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] voxel vs surface based morphometric analysis
Hi Doug, I ran voxel based analysis in FSL to check the differnce in PET signal between two groups. The results are totally differnt than surface based analysis in Freesurfer. I this real or I am doing something wrong? I tried to do the same but using FA maps and also I got totally differnt results. I have special interest in understanding why these two methods leads to differnt results?! I have read this refernce http://cds.ismrm.org/protected/11MProceedings/files/ISMRM2011-8410.pdf and actually I was unable to reach the point that can explain this differnce in th results. I highly appreciate if you clarify that to me. Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_glmfit
Hi Experts, What is the meaning of this error as an output of the command mri_glmfit Found 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input in other words what are therrors that can lead to such like error message Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer
Thank you doug, Please what do you suggesst me to do? Is this related to something wrong in the analysis? Bests, John Sent: Wednesday, March 16, 2016 at 10:42 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer it looks like the cluster is covering most of the brain, including precentral gyrus. The precentral gyrus ROI in the table file indicates that is where the peak of the cluster is and does not mean that the cluster is confined to that ROI On 3/16/16 9:43 AM, John Anderson wrote: Dear experts, I am running into a trouble visualizing my data in tksurfer. I highly appreciate any advice that can help! I ran group analysis between two groups using GLM analysis (mri_glmfit) and I corrected the results for multiple comparison using (mri_glmfit-sim), then I ran this command to visualize the results: tksurfer fsaverage lh inflated -overlay cache.th13.pos.sig.cluster.mgh The result attached. In my summary file I see that I have significant differnce only in the precentral gyrus. But the results in tksurger is not showing precentral gyrus. I tried to play with the thresholds and nothing changed. Any advice is highly appreciated!! Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_fwhm
Hi FS experts, I am trying to use the folowing command: mri_fwhm --i lh.mgh --auto-mask 0.2 --sum lh.fwhm5.sum --fwhm 5 --o lh_5mm.mgh I keep receiving an error message as follow: voxelvolume 1 mm3 Computing mask, relative threshold = 0.2, gmean = 0.501858, absthresh = 0.100372 Search region is 163842 voxels = 163842.00 mm3 Polynomial detrending, order = 0 Detrending Smoothing input by fwhm=5.00, gstd=2.123305 Segmentation fault (core dumped) Any suggestion? Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] longitudinal data analysis
Hi Dr Martin I want to study the change in cortical thickness overtime in one group of subjects. I have only one group of subjects who scanned multiple times ( two time points and more) I followed the pipeline exactly as in wiki. I want to inquire about X in this case . Is it supposed to be 1 ( one group) In wiki they used the follwoing x=[ones(length(M),1) M M(:,1).M*(:2)] how this formulla will be for one group of subjects? Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] longitudinal data analysis
Dear Dr Martin, Thanks you very much for your awesome clarification and your kindness!! Bests, John Hi John, X is the design matrix. The rows are the total number of time points for all subjects, the columns the different parameters of your model. In the wiki example, the first column is all 1s (intercept) the second is the time_from_baseline and other parameters that are in the matrix M (M was read from the qdec table file), the last column is the interaction between the first and second column in M (so probably time X group interaction). So for you, you probably have column of ones, time_from_baseline and potentially other control variables (age_at_baseline, gender, scores? IQ.. whatever you want). Only having 2 columns (ones for the intercept and time for the slope) allow you to test - if whatever you test is different from zero (intercept), usually that is the case, as you measure volume or thickness - if the longitudinal slope is different from zero, usually that is also the case, but sometimes you don't have enough power to find that effect. So that does not really tell you much. For most interesting questions you need two groups. Best, Martin On 03/21/2016 12:40 PM, John Anderson wrote: Hi Dr Martin I want to study the change in cortical thickness overtime in one group of subjects. I have only one group of subjects who scanned multiple times ( two time points and more) I followed the pipeline exactly as in wiki. I want to inquire about X in this case . Is it supposed to be 1 ( one group) In wiki they used the follwoing x=[ones(length(M),1) M M(:,1).M*(:2)] how this formulla will be for one group of subjects? Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] V1 Atlas ( brodman maps)
Dear experts, I want to use the atlas V1 to calculate PET signal for Brodman areas. How can I create this atlas in the form of “aseg.mgz” or ”wmparc.mgz” ( i.e all the BAs in one file) to feed it in the command “mri-segstat”? Bests, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] V1 Atlas ( brodman maps)
Thank you Dr Bruce, I want to calculate PET signal in each Brodman map! I will give an example: If I want to caclulate PET singal for every parcellate and segment in the atlas "wmparc.mgz". I do the following: bbregister --t1 --mov T1.nii.gz --init-fsl --reg t1.reg.dat --s SUBJID mri_vol2vol --mov PET_MAP.nii --reg t1.reg.dat --fstarg --interp nearest --o PET_MAP.anat.nii mri_segstats --seg $SUBJECTS_DIR/SUBJID/mri/wmparc.mgz --ctab-default --i PET_MAP.anat.nii --mask PET_MAP.anat.nii --sum PET_MAP.summary.dat How can I do the same previous steps ( if correct) on the atlas V1. I.e how can I replace the atalas "wmparc" in the command "mri_segstat" with the atals V1 to get PET signal for every brodman? Bests, John Sent: Wednesday, May 11, 2016 at 8:10 PM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] V1 Atlas ( brodman maps) Hi John recon-all should create lh.BA.annot and rh.BA.annot parcellations that contain all the Brodmann areas we know how to label cheers Bruce On Thu, 12 May 2016, John Anderson wrote: > Dear experts, > I want to use the atlas V1 to calculate PET signal for Brodman areas. How > can I create this atlas in the form of “aseg.mgz” or ”wmparc.mgz” ( i.e all > the BAs in one file) to feed it in the command “mri-segstat”? > Bests, > John > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] V1 Atlas ( brodman maps)
Dear Experts, I want to calculate PET signal within each Brodman map! I will give an example: If I want to caclulate PET singal for every parcellate and segment in the brain I do the following: bbregister --t1 --mov T1_MPRAGE.nii.gz --init-fsl --reg t1.reg.dat --s SUBJID mri_vol2vol --mov PET_MAP.nii --reg t1.reg.dat --fstarg --interp nearest --o PET_MAP.anat.nii mri_segstats --seg $SUBJECTS_DIR/SUBJID/mri/wmparc.mgz --ctab-default --i PET_MAP.anat.nii --mask PET_MAP.anat.nii --sum PET_MAP.summary.dat How can I do the same previous steps ( or something similar) on the atlas V1. I.e how can I replace the atalas "wmparc" in the command "mri_segstat" with the atals V1 to get PET signal for every brodman?. I can't locate the atals V1 as a file like wmparc.mgz or aseg.mgz is there any method to creat this atlas? Many thanks for any advice! John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] surface based analysis
Hello Freesurfers, I am working on a PET surface based analysis between two groups. I did the following: 1. I concatentaed the PET images using the command "mris_preproce" and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right hemisphere. 2. I smoothed "lh.mgh and rh.mgh) using the command: mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.mgh --tval lh_sm10.mgh 3. I studdied the diffence between the groups usiing the command: mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf fsaverage lh --cortex --glmdir lh 4. I corrected the results for multiple comparison using the command: mri_glmfit-sim --glmdir lh --cache 30 pos --cwp 0.01 --2spaces I want to narrow (reduce the strictness) of the correction for multiple comparision to a specific label (e.g. precentral gyrus). I changed the commands "mri_glmfit" and "mri_glmfit-sim" as follow: mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf fsaverage lh --label precentral --glmdir lh mri_glmfit-sim --glmdir lh --cache 30 pos --cache-label precentral --cwp 0.01 --2spaces I got error that the label "precentral" is not exist. I was unable to find this label in the folder "fsaverage". Kindly: 1. whct I am doing wrong? 2. How can I create this label ? and in whcih folder it must be placed? Best, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] surface based analysis
Thank you Doug, Actually I was trying to apply what was mentioned in this link by replicating the method on the command "mri_glmfit" and not using the command "mri_mcsim". I tried to use for example the label "BA4a" (it is available in the folder/fsaverage/label), but the command "mriglm_fit failed to see it!! I ran the command as follow: mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf fsaverage lh --label BA4a --glmdir lh Kindly, what I am doing wrong in this command ? and how can I create label? What command I need? Can I use mri_binarize for example and save the output as a label? John Sent: Thursday, January 26, 2017 at 1:15 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface based analysis FS does not come with correction tables for all labels. You'll have to build your own. here are the instructions: http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo On 01/26/2017 01:09 PM, John Anderson wrote: > Hello Freesurfers, > I am working on a PET surface based analysis between two groups. I did > the following: > 1. I concatentaed the PET images using the command "mris_preproce" > and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right > hemisphere. > 2. I smoothed "lh.mgh and rh.mgh) using the command: > mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.mgh --tval > lh_sm10.mgh > 3. I studdied the diffence between the groups usiing the command: > mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf > fsaverage lh --cortex --glmdir lh > 4. I corrected the results for multiple comparison using the command: > mri_glmfit-sim --glmdir lh --cache 30 pos --cwp 0.01 --2spaces > I want to narrow (reduce the strictness) of the correction for > multiple comparision to a specific label (e.g. precentral gyrus). I > changed the commands "mri_glmfit" and "mri_glmfit-sim" as follow: > mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf > fsaverage lh --label precentral --glmdir lh > mri_glmfit-sim --glmdir lh --cache 30 pos --cache-label precentral > --cwp 0.01 --2spaces > I got error that the label "precentral" is not exist. I was unable to > find this label in the folder "fsaverage". Kindly: > 1. whct I am doing wrong? > 2. How can I create this label ? and in whcih folder it must be placed? > Best, > John > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] bbregister
Hi FS experts, I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using the command bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj do I need to apply brain extraction tools before this step or bb register can accept non-brain extracted images? Best, John ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fw: Re: bbregister
Thank you very much! Kindly, I have one follow up question: I have VOI 20X20X20 mm have been created during an MR spectroscopy session. This VOI was placed in specific loacation on the T1 image. I have created this VOI using the command "mri_volsynth" and I want to move it from native space (T1) to Freesurfer space (e.g. wmparc.mgz) so I can generrat somestatistics using the command "mri_segstats". I ran the following commands: bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj tkregister2 --mov VOI.nii --int T1.nii t1.reg.dat --reg VOI.reg.dat --noedit --subject subj mri_vol2vol --mov VOI.nii --reg t1.reg.dat --fstarg --interp nearest --o VOI.anat.nii Are these stpes correct? When I open T1.nii and the VOI.nii in freeview, I can see the VOI in it is correct position. But when I open "wmparc.mgz" and "VOI.anat.nii" then VOI is not showing in the correct position. I suspet that I am doing something wrong in the previous steps and I highly appreciate any feedback! Best, John For version 6, it should not matter. Sent: Friday, February 10, 2017 at 4:03 PM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] bbregister Hi John one of the many nice things about bbregister is that it is quite resistant to non-brain tissue, since it's just trying to place the gray/white (and optionally the pial surface) at a reasonable spot in the volume. I guess it might make the initialization less robust, not sure, but I expect it works pretty well without doing brain extraction cheers Bruce On Fri, 10 Feb 2017, John Anderson wrote: > Hi FS experts, > I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using > the command > bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj > > do I need to apply brain extraction tools before this step or bb register > can accept non-brain extracted images? > > Best, > John > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] bbregister
Thank you very much! Kindly, I have one follow up question: I have VOI 20X20X20 mm have been created during an MR spectroscopy session. This VOI was placed in specific loacation on the T1 image. I have created this VOI using the command "mri_volsynth" and I want to move it from native space (T1) to Freesurfer space (e.g. wmparc.mgz) so I can generrat somestatistics using the command "mri_segstats". I ran the following commands: bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj tkregister2 --mov VOI.nii --int T1.nii t1.reg.dat --reg VOI.reg.dat --noedit --subject subj mri_vol2vol --mov VOI.nii --reg t1.reg.dat --fstarg --interp nearest --o VOI.anat.nii Are these stpes correct? When I open T1.nii and the VOI.nii in freeview, I can see the VOI in it is correct position. But when I open "wmparc.mgz" and "VOI.anat.nii" then VOI is not showing in the correct position. I suspet that I am doing something wrong in the previous steps and I highly appreciate any feedback! Best, John For version 6, it should not matter. Sent: Friday, February 10, 2017 at 4:03 PM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] bbregister Hi John one of the many nice things about bbregister is that it is quite resistant to non-brain tissue, since it's just trying to place the gray/white (and optionally the pial surface) at a reasonable spot in the volume. I guess it might make the initialization less robust, not sure, but I expect it works pretty well without doing brain extraction cheers Bruce On Fri, 10 Feb 2017, John Anderson wrote: > Hi FS experts, > I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using > the command > bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj > > do I need to apply brain extraction tools before this step or bb register > can accept non-brain extracted images? > > Best, > John > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_segstats
Dear Freesurfer experts, I have used the following commandline to generate the final statistics in my analysis: mri_segstats --seg aseg.mgz --ctab-default --i suvr.nii --mask mask.nii --sum stats.dat The final output of this command is (attached). Depedning on the anatomical location of the mask, I expect that I will get two structures in the stats file. What is the "unknown" label means? is it CSF? Do I need to include it in my next statistcal analses? I highly appreciate your input! Best, John Sent with [ProtonMail](https://protonmail.com) Secure Email.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] bbregister vs spmregister vs mri_coreg
Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differences ? 2. Is there any preference of using a tool over the others for specific type of data. For example: A. If I want to register FA map to T1 image which tool is more robust? B. if I want to register FA map to MNI space which tool is more robust? I highly appreciate your input on this! John___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] bbregister vs spmregister vs mri_coreg
Hi Doug, thank you for the detailed response. Highly appreciated! Kindly. I want to register FA map to structural T1 image using the command mri_spmregister as follow: mri_spmregister move FA.nii --s subj1 --reg reg dat --o FA_2_T1.nii.gz Is this correct? Original Message Subject: bbregister vs spmregister vs mri_coreg Local Time: February 25, 2017 8:49 AM UTC Time: February 25, 2017 1:49 PM From: john.ande...@protonmail.com To: freesurfer@nmr.mgh.harvard.edu mri_coreg is the FS implementation of spm_coreg (spmregister) both of which use normalized mutual info. bbregister uses the BBR cost function and is preferred for all MRI. For registration to MNI space, we usually use mni152reg (a wrapper around fsl's flirt) On 2/25/17 8:49 AM, John Anderson wrote: Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differences ? 2. Is there any preference of using a tool over the others for specific type of data. For example: A. If I want to register FA map to T1 image which tool is more robust? B. if I want to register FA map to MNI space which tool is more robust? I highly appreciate your input on this! John t?e�?�Z� Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differences ? 2. Is there any preference of using a tool over the others for specific type of data. For example: A. If I want to register FA map to T1 image which tool is more robust? B. if I want to register FA map to MNI space which tool is more robust? I highly appreciate your input on this! John___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Reslice image
Dear experts: I have nifti file with 96 slices. I want to re-slice it to form nifti file with 200 slice. Are there any tools in Freesurfer that can help to achieve this? Many thanks for any suggestion John___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Moving fa map from talairach to MNI
Hi Freesurfer experts, I followed "dt_recon" pipeline https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon to analyze DTI data. The analysis ran smoothly without any issues. I want to inquire waht is the correct method to move "fa-tal.nii" to MNI152_2mm Is this command correct"? mri_vol2vol --mov fa-tal.nii --targ MNI152_2mm --regheader --o fa-MNI --no-save-reg Thank you for any advice John Sent with [ProtonMail](https://protonmail.com) Secure Email.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FW: MPRAGE images dimension different {Disarmed}
Dear Dhaval, when your recon-all finishs the process you will get images 256^3 and 1mm isootropic. The you can simply follow the instructions mentioned here https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat to send your images back to native space. All the best, John > > On Mon, Apr 3, 2017 at 4:35 PM, Dhaval Shah wrote: > Hi All, > > I am new and a very basic question about freesurfer processing. > > I ran recon-all on a high res-T1 image(128x128x80 matrix size), but > after recon-all the folder mri contains resulted (brain.mgz and > orig.mgz) T1 images has (127x128x128 matrix size). > > 1) how come the dimensions are changed? Is it normal? > 2) how can i keep the dimensions same as the original? > 3) is it possible that i will always get the higher matrix size image > data? > > for simplicity, i converted resulted orig.mgz to nii format and loaded > it in to fslview. Please find the first image (Original) and the > second image (after recon-all but orig.mgz). > > Your help is greatly appreciated. > > -- > Kind regards, > Dhaval Shah > > MRI Research fellow,MRI Physicist,Clinical Trial Research Staff > Buffalo Neuroimaging Analysis Center > State University of New York at Buffalo > Department of Neurology > 100 High St., D-2, Buffalo, NY 14203 > [MailScanner has detected a possible fraud attempt from "ds...@bnac.net" > claiming to be MailScanner has detected a possible fraud attempt from > "ds...@bnac.net" claiming to be > ds...@bnac.net//http://mbl.bnac.net](http://ds...@bnac.net/http:/mbl.bnac.net) > > > > > -- > Kind regards, > Dhaval Shah > > MRI Research fellow,MRI Physicist,Clinical Trial Research Staff > Buffalo Neuroimaging Analysis Center > State University of New York at Buffalo > Department of Neurology > 100 High St., D-2, Buffalo, NY 14203 > [MailScanner has detected a possible fraud attempt from "ds...@bnac.net" > claiming to be MailScanner has detected a possible fraud attempt from > "ds...@bnac.net" claiming to be > ds...@bnac.net//http://mbl.bnac.net](http://ds...@bnac.net/http:/mbl.bnac.net) > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Kind regards, Dhaval Shah MRI Research fellow,MRI Physicist,Clinical Trial Research Staff Buffalo Neuroimaging Analysis Center State University of New York at Buffalo Department of Neurology 100 High St., D-2, Buffalo, NY 14203 ds...@bnac.net // http://mbl.bnac.net___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Volume vs cortical thickness
Dear Freesurfer experts, I highly appreciate if anybody clarify how Freesurfer calculate cortical thickness and gray matter volume. If the cortical thickness of e.g. precentral gurus is measured as the closest distance from the gray-white boundary to the gray-CSF boundray at each vertex on the tessellated surface (Fischl and Dale. 2000). How the gray matter volume for the precentral gyrus was measured? Thank you for any clarification! John___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] manual edits
Hi David, Thank you for the feedback! I followed your advice's and everything has been resolved. Highly appreciated! Cheers, John Sent with [ProtonMail](https://protonmail.com) Secure Email. Original Message Subject: Re: [Freesurfer] manual edits Local Time: April 12, 2017 11:04 AM UTC Time: April 12, 2017 3:04 PM From: seman...@nyspi.columbia.edu To: John Anderson , freesurfer@nmr.mgh.harvard.edu Hi John, Yes understanding how freesurfer deals with edits can be a bit confusing. I have a lot of experience doing edits to the wm.mgz and brainmask.mgz for cross sectional data in Freesurfer 5.3 so perhaps I can help. Recon-all is basically a script which runs a series of about 25 or so processing steps in a defined sequence. The software generally will be able to recognize when an edit has been done at a particular intervention point and will take those edits into account when running that step unless you specifically instruct it not to. The most common types of edits are edits to the wm.mgz to fix white matter defects and tissue incorrectly identified as white matter, and edits to the brainmask.mgz to fix cases where the skull strip is insufficient to prevent dura and other non-cortical tissue from making it into the gray matter/pial surfaces. White matter edits need to be done directly on the wm.mgz and gray matter/skull strip edits need to be done on the brainmask.mgz. Editing those two files and saving them directly in freeview is sufficient to register those edits for recon-all. If you have edited only the brainmask.mgz, it is sufficient to run –autorecon-pial since the white matter surfaces will not need to be regenerated. If you have edited the wm.mgz, you must run –autorecon2-wm (or –autorecon2-cp if you used control points as well as white matter edits). If you have edited both the brainmask.mgz and the wm.mgz, then you only need to run –autorecon2-wm since the pial surfaces will be regenerated taking into account the brainmask.mgz edits as part of that workflow. Keep in mind that you still need to run –autorecon3 to complete the reprocessing of these data (-autorecon-pial includes the steps from –autorecon3) but that can be done when you are happy with your final surfaces if you want to save processing time on iterative edits. Here is the wiki page referring to edits: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData I hope this is helpful. Best, David P. Semanek, HCISPP Research Technician, Posner Lab Division of Child and Adolescent Psychiatry Columbia University Medical Center New York State Psychiatric Institute 1051 Riverside Drive, Pardes Bldg. Rm. 2424 New York, NY 10032 PH: (646) 774-5885 IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From: John Anderson Reply-To: John Anderson Date: Wednesday, April 12, 2017 at 6:45 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] manual edits Dear Freesurfer experts, I am not an expert in manual edits, so I highly appreciate any feedback regarding the issues in my questions below. I ran the following command line “recon-all -s subjid -all” on T1 image for one of the subjects. when reviewing the output images (i.e. wm.mgz, brainmask.mgz) I found issues as attached. Attached is an output of the command: "Freeveiw orig.mgz wmparc.mgz wm.mgz" 1. When I reviewed “wm.mgz” I see interactions between the white matter (wm), and the cortex (yellow arrows). To fix this, I edited “wm.mgz” by removing the wm voxels from the cortex, and the data was saved in the file “wm.seg.mgz” 2. I found many holes in many slices similar to the (black arrow). I filled all these holes. The data saved in “wm.seg.mgz” 3. I fixed some issues related to dura and bad skullstipping Then I ran the command: “recon-all -autorecon2-wm -autorecon3 -subjid ” which output the file “brain.finalsurfs.mgz” and the command “recon-all -autorecon-pial -subjid ” Now, I want to understand where Freesurfer implement the new edits? Which files will be used as the main files that include the new edits. Logically, the edits must be implemented in "wm.mgz" and "brainmask.mgz". What confuses me is when I open orig.mgz wm.mgz and brainmask.mgz in freesview. I see the original non-edited files. I am not sure what I am doing wrong so I highly appreciate any help. John___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu http
[Freesurfer] White matter atrophy
Dear Freesurfer experts, I know how to do cortical thickness group analysis using Freesurfer, also I know how to use Qdec to compare groups regarding gray matter volume differences, cortical thickness, curvatures, area,... etc. I am wondering if there is any way in Freesurfer to study the difference in white matter volume between two groups? I highly appreciate any suggestion! John___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
