Re: [Freesurfer] Extraction of segmentation maps using mri_extract_label
for left and right: 1. 2 and 42 2. 3 and 42 3. 10 and 49 4. 77/78/79 5. 11 and 50 6. 12 and 51 7. 13 and 52 8. We don't have a single one for all of cingulate and it depends on which parcellation you use. You should take the uniton of e.g. 1002 and such (assuming you are using the aparc and not the a2009) cheers Bruce On Wed, 7 Jan 2015, Ben Eliezer, Noam wrote: Dear Freesurfer Gurus — I’m using mri_extract_label to extract segmentation masks, but a little baffled as to which label numbers to use for each brain part. The masks I need are: 1. Global white matter 2. Cortical Gray matter 3. Thalamus 4. WM-Hypointensity 5. Caudate nucleus 6. Putamen 7. Palidum 8. Entire cingulate gyrus ...the problem is each of these appear under many label numbers. For example, the thalamus appears in label numbers: 9, 10, 48, 49, 107, 116, 8001-8014. Any suggestion how to decide which label numbers to use for each of the above brain parts? Thanks! — Noam -- Noam Ben-Eliezer, PhD Adjunct Assistant Professor of Radiology Center for Biomedical-Imaging New-York University Medical School noam.ben-elie...@nyumc.org ___ 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] Meninges labelled as cortex
Hi Amanda it depends what you are doing. They will certainly distort thickness estimates in those regions. It is really, really hard to get rid of dura unless you acquire data for that purpose. If you have a highres FLAIR or T2 or a multi-echo mprage we have tools for automatically avoiding it. cheers Bruce On Wed, 7 Jan 2015, Worker, Amanda wrote: Hi All, I have noticed that almost all of my data has some voxels of dura that have incorrectly been labelled as cortex. It doesn't look like a severe problem and I've attached a screen shot to show you. I'm just wondering whether this is something that will affect my results? I have tried using -gcut and adjusting the watershed parameters to a height of 24, but nothing seems to work. As I have many subjects it would be very time consuming to manually adjust all of these voxels. Do you think this poses a problem or can I leave it as it is? Best wishes, Amanda ___ 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] Hyperintense WM & WM Deletions
tentorium is tough depending on the details of the scan good luck Bruce On Wed, 7 Jan 2015, Douglas Merkitch wrote: Hello Bruce, Thanks for the suggestion! I've never used control points to bring intensities down, but I suppose they do normalize the selected voxels to an intensity value of 110. There are also a few voxels of what to my eyes appear to be tentorium that are labeled as white matter. Can you think any good way to exclude said voxels? I will also take you up on your offer and upload the subject directory. Thanks again for the help! Doug Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: douglas_merki...@rush.edu On Jan 6, 2015, at 7:39 AM, Bruce Fischl wrote: Hi Anthony and Doug have you tried control points? If you upload a subject dir I'll take a look cheers Bruce On Mon, 5 Jan 2015, Anthony Dick wrote: We have the same problem using the same coil (GE 750; mainly occipital pole), so any suggestions for how to correct this would be very helpful. Thanks! Anthony On 1/5/15, 7:05 PM, Douglas Merkitch wrote: Hello Freesurfer experts, We have T1 data from a 3T GE 32-channel head coil that exhibits areas of hyperintense white matter. Specifically there are areas of the wm.mgz on the periphery with values ranging from 117-121, which lead to overextending/overestimation of the wm.mgz. 1) Can anyone suggest specific processing options or flags to help correct for peripheral hyperintense white matter? 2) Can anyone suggest methods of correcting for local overestimation of white matter on the periphery? Your help is greatly appreciated! Doug Doug Merkitch Neurological Sciences Rush University Medical Center ___ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly 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] Hyperintense WM & WM Deletions
p.s. although labeling tentorium as wm shouldn't matter as long as there is no connection to the body of the cerebral wm On Wed, 7 Jan 2015, Douglas Merkitch wrote: Hello Bruce, Thanks for the suggestion! I've never used control points to bring intensities down, but I suppose they do normalize the selected voxels to an intensity value of 110. There are also a few voxels of what to my eyes appear to be tentorium that are labeled as white matter. Can you think any good way to exclude said voxels? I will also take you up on your offer and upload the subject directory. Thanks again for the help! Doug Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: douglas_merki...@rush.edu On Jan 6, 2015, at 7:39 AM, Bruce Fischl wrote: Hi Anthony and Doug have you tried control points? If you upload a subject dir I'll take a look cheers Bruce On Mon, 5 Jan 2015, Anthony Dick wrote: We have the same problem using the same coil (GE 750; mainly occipital pole), so any suggestions for how to correct this would be very helpful. Thanks! Anthony On 1/5/15, 7:05 PM, Douglas Merkitch wrote: Hello Freesurfer experts, We have T1 data from a 3T GE 32-channel head coil that exhibits areas of hyperintense white matter. Specifically there are areas of the wm.mgz on the periphery with values ranging from 117-121, which lead to overextending/overestimation of the wm.mgz. 1) Can anyone suggest specific processing options or flags to help correct for peripheral hyperintense white matter? 2) Can anyone suggest methods of correcting for local overestimation of white matter on the periphery? Your help is greatly appreciated! Doug Doug Merkitch Neurological Sciences Rush University Medical Center ___ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly 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] R: Re: R: Error first step FS-FAST
ls -l and see if the 'x' bit is set. For example: ls -l mris_register mris_register.c -rwxrwxr-x 1 fischl fsdev 21563282 Jan 6 17:02 mris_register -rw-rwxrw- 1 fischl fsdev37035 Jan 6 17:02 mris_register.c mris_register.c is not and mris_register is executable cheers Bruce On Wed, 7 Jan 2015, std...@virgilio.it wrote: How can I check whether it is executable? Thanks, Setafno Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 7-gen-2015 22.51 A: Ogg: Re: [Freesurfer] R: Error first step FS-FAST And is it executable? On 01/07/2015 04:35 PM, std...@virgilio.it wrote: > > Thank you very much. > > I have placed file 3dvolreg.afni in Applications/freesurfer/bin/ but > the error persist. > > Stefano > > > > Messaggio originale > Da: std...@virgilio.it > Data: 7-gen-2015 11.14 > A: > Ogg: [Freesurfer] Error first step FS-FAST > > Hi list, > > I'm running FS-FAST. > > After this command > > preproc-sess -sf sessid -surface fsaverage lhrh -mni305 -fwhm 5 > -per-run -fsd rest > > I obtain this error: > > register-sess completed > > Sess01 MC - > > mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d > /Applications/freesurfer/subjects/FUNCTIONAL_DATA -fsd rest -per-run > -update > > Logfile is > /Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/mc-Sess01-rest.log > > --- > > /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01 > > RunList: 001 002 003 > > --- ** --- > > --- Motion Correcting Run 001 --- > > --- ** --- > > sess = Sess01 > > Wed Jan 7 11:07:02 CET 2015 > > mc-afni2 --i 001/f.nii --t 001/template.nii.gz --o 001/fmcpr.nii.gz > --mcdat 001/fmcpr.mcdat > > ERROR: cannot find AFNI command 3dvolreg.afni > > > What is 3dvolreg.afni? Where it should be placed? > > > > Thanks in advanced > > > > Stefano > > > > > > > > ___ > 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] Texture Features
Hi Raunak I've messed around with this a bit, but never wrote anything that would be usable by anyone else. The individual steps aren't that hard though if you want to write it yourself using our outputs. We are happy to point you in the right direction if so. cheers Bruce On Thu, 8 Jan 2015, Raunak Mundada wrote: Hi I have been trying to compute some texture features using a 3D mri scan using GLCM technique. Unfortunately haven’t come across much literature or standard toolboxes to do so. Do you guys happen to know any? To be precise, the procedure that I intend to follow - 1. Use recon-all process on the original mri scan 2. Using files like left_hippocampus.nii ( which look like just masks to me), create a gray scale image of the left hippocampus. 3. Use this gray-scale image to construct co-occurrence matrix. 4. Compute the corresponding Haralick features I want these features for the 3D image itself. Is there a way to carry out the complete process mentioned above in Freesurfer itself? Or any other software/toolbox that can be combined with freesurfer? Appreciate any help. Regards, Raunak Mundada [avast-mail-stamp.png] This email is free from viruses and malware because avast! Antivirus protection is active. ___ 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 error
Hi Mia can you send us the recon-all.log? I don't think you included the error message in your email so there isn't much for us to go on. thanks Bruce On Thu, 8 Jan 2015, Borzello, Mia wrote: Hi Freesurfers, I'm wondering if you can help with the following error that occurred when trying to create a reconstruction: FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects 1)BI22 2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject BI22_SurferOutput -i/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_BI19/4571 /4571157.dcm 3)recon-all -s exited with ERRORS at Thu Jan 8 13:08:33 EST 2015 Thanks, m ___ 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 error
did you look in /autofs/space/huygens_001/users/mia/subjects Can you send us the screen output of recon-all? On Thu, 8 Jan 2015, Borzello, Mia wrote: > I looked for that file and did not see a BI22_SurferOutput folder at all. > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, January 08, 2015 2:34 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all error > > Hi Mia > > can you send us the recon-all.log? I don't think you included the error > message in your email so there isn't much for us to go on. > > thanks > Bruce > > On Thu, 8 Jan 2015, Borzello, Mia wrote: > >> >> Hi Freesurfers, >> >> I'm wondering if you can help with the following error that occurred when >> trying to create a reconstruction: >> >> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 >> >> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >> >> RedHat release: CentOS release 6.5 (Final) >> >> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 >> >> NMR Center info (/space/freesurfer exists): >> >> machine: huygens >> >> SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects >> >> PWD: /autofs/space/huygens_001/users/mia/subjects >> >> ssh huygens >> setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects >> cd /autofs/space/huygens_001/users/mia/subjects >> >> >> 1)BI22 >> 2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject BI22_SurferOutput >> -i/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_BI19/4571 >> /4571157.dcm >> 3)recon-all -s exited with ERRORS at Thu Jan 8 13:08:33 EST 2015 >> >> >> Thanks, >> m >> >> > > ___ > 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] Texture Features
Hi Raunak you can extract any label you want from files like aparc+aseg.mgz using mri_extract_label or mri_binarize --match. Or you can just load the label and intensity volumes into matlab and compute co-occurrence matrices there easily using find and such. cheers Bruce On Fri, 9 Jan 2015, Raunak Mundada wrote: Hi Bruce, Thank you. Would need help from you guys. Firstly, I would like to clarify from you if I am on the right path with respect to the procedure that I intend to follow? I mean a file like left_hippocampus.nii is the right output to go for or is there any other output from FreeSurfer that would be a better approach to this problem? Any software that you suggest would be good for this purpose? My ultimate goal is to compute a lot of textual features (like the wavelet based ones) but the immediate goal is to extract the Haralick features which seem easy to compute to begin with. If not this approach, then how do you suggest I should go about it? Regards, Raunak From: Raunak Mundada [mailto:rmund...@algoanalytics.com] Sent: Thursday, January 08, 2015 5:40 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Texture Features Hi I have been trying to compute some texture features using a 3D mri scan using GLCM technique. Unfortunately haven’t come across much literature or standard toolboxes to do so. Do you guys happen to know any? To be precise, the procedure that I intend to follow - 1. Use recon-all process on the original mri scan 2. Using files like left_hippocampus.nii ( which look like just masks to me), create a gray scale image of the left hippocampus. 3. Use this gray-scale image to construct co-occurrence matrix. 4. Compute the corresponding Haralick features I want these features for the 3D image itself. Is there a way to carry out the complete process mentioned above in Freesurfer itself? Or any other software/toolbox that can be combined with freesurfer? Appreciate any help. Regards, Raunak Mundada [avast-mail-stamp.png] This email is free from viruses and malware because avast! Antivirus protection is active. ___ 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] Openmp option does not work in Ubuntu 12.04
Hi Krishnaprasad what is your full recon-all command line? And how do you know it isn't working? Have you tried running "top" during the mri_ca_register stage? The upcoming (one of these months!) release will have much more in the way of openmp optimization cheers Bruce On Mon, 12 Jan 2015, Narayanan, Krishnaprasad wrote: Hallo all, I have installed freesurfer v5.3 on Ubuntu 12.04 LTS. The GCC version is 4.6. I use the recon-all using –all and -openmp option. I observed that openmp does not seem to have any effect in the execution of freesurfer. I verified the installation of openmp using dpkg --status libgomp1 and found that the package was installed. Do I have to install or enable any additional library or flags? Can I kindly get help from the forum to resolve this problem? Best regards, Krishnaprasad ___ 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] Texture Features
Hi Raunak it isn't a straight (binary) mask - it's a label map. You can use it to determine what voxels are in e.g. the left hippocampus (label == 17) then use the norm.mgz to compute the intensity co-occurrence map cheers Bruce On Mon, 12 Jan 2015, Raunak Mundada wrote: Hi Bruce I am attaching a view of the aparc+aseg.mgz file. Is this the expected output? I am slightly confused here because this looks a like a mask to me. So when I use the mri_extract_label command to extract say the left hippocampus, I have gotten a 256*256*256 binary image of the left hippocampus. But from this we cant compute the co-occurrence matrix right? Please correct me if I am wrong anywhere. Regards, Raunak -Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, January 09, 2015 7:27 PM To: Raunak Mundada Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Texture Features Hi Raunak you can extract any label you want from files like aparc+aseg.mgz using mri_extract_label or mri_binarize --match. Or you can just load the label and intensity volumes into matlab and compute co-occurrence matrices there easily using find and such. cheers Bruce On Fri, 9 Jan 2015, Raunak Mundada wrote: Hi Bruce, Thank you. Would need help from you guys. Firstly, I would like to clarify from you if I am on the right path with respect to the procedure that I intend to follow? I mean a file like left_hippocampus.nii is the right output to go for or is there any other output from FreeSurfer that would be a better approach to this problem? Any software that you suggest would be good for this purpose? My ultimate goal is to compute a lot of textual features (like the wavelet based ones) but the immediate goal is to extract the Haralick features which seem easy to compute to begin with. If not this approach, then how do you suggest I should go about it? Regards, Raunak From: Raunak Mundada [mailto:rmund...@algoanalytics.com] Sent: Thursday, January 08, 2015 5:40 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Texture Features Hi I have been trying to compute some texture features using a 3D mri scan using GLCM technique. Unfortunately haven?t come across much literature or standard toolboxes to do so. Do you guys happen to know any? To be precise, the procedure that I intend to follow - 1. Use recon-all process on the original mri scan 2. Using files like left_hippocampus.nii ( which look like just masks to me), create a gray scale image of the left hippocampus. 3. Use this gray-scale image to construct co-occurrence matrix. 4. Compute the corresponding Haralick features I want these features for the 3D image itself. Is there a way to carry out the complete process mentioned above in Freesurfer itself? Or any other software/toolbox that can be combined with freesurfer? Appreciate any help. Regards, Raunak Mundada [avast-mail-stamp.png] This email is free from viruses and malware because avast! Antivirus protection is active. 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. --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com ___ 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] GCA file
Hi Sophie what kind of modifications did you make? The 3 volumes are part of the information in the gca, but not all of it (they don't contain the markov information) so there is no way to recreate it from only them. mri_ca_train is the only way to make a gca at the moment, although there is some matlab code around I think cheers Bruce On Mon, 12 Jan 2015, Sophie Maingault wrote: Dear experts, I extracted the 3 mgz volumes of the GCA file used in the recon-all process (RB_all_2008-03-26.gca). I modified these files and I wanted to recreate the GCA file by reunite the 3 mgz. I tried some mri_convert command but I failed to convert these 3 volumes in 1 GCA file. Is it possible to do it ? Regards, Sophie Maingault – Doctorante/PhD student GIN (Groupe d'Imagerie Neurofonctionnelle) UMR 5296 – Université de Bordeaux – CNRS/CEA 146, rue Léo Saignat – Case 71 33076 Bordeaux cedex ___ 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] Fwd: Intersection of gray matter and white matter lines - Question
Hi Christina I think this is something that is fixed in the new version. If you want a patch we can send you new versions of recon-all and mris_make_surfaces cheers Bruce On Sat, 10 Jan 2015, Christina Chen wrote: On Dec 24, 2014, at 10:44 PM, Christina Chen wrote: > Hi! > > When looking through the brain scans, I've noticed that the lines outlining white matter intersect with lines outlining the gray matter. Any suggestions on how I fix this problem? > > Thanks, > Christina > ___ > 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 error
does that dicom exist? Can you run ls -l on it? On Sat, 10 Jan 2015, Borzello, Mia wrote: > I just fixed that but I'm still getting an error. I attached a screenshot. > > Thanks, > Mia > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Krieger, Donald N. > [krieg...@upmc.edu] > Sent: Friday, January 09, 2015 5:39 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all error > > It looks like there's a typo in your recon-all command - there's a space > between "-" and autorecon3 . > > Regards, > > Don > > > Don Krieger, Ph.D. > Department of Neurological Surgery > University of Pittsburgh > (412)648-9654 Office > (412)521-4431 Cell/Text > > >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- >> boun...@nmr.mgh.harvard.edu] On Behalf Of Borzello, Mia >> Sent: Friday, January 09, 2015 5:30 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all error >> >> Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects. >> I attached the output error for recon-all. >> >> Thanks, >> m >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer- >> boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Thursday, January 08, 2015 4:27 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all error >> >> did you look in >> >> /autofs/space/huygens_001/users/mia/subjects >> >> Can you send us the screen output of recon-all? >> >> On Thu, 8 Jan 2015, Borzello, >> Mia wrote: >> >>> I looked for that file and did not see a BI22_SurferOutput folder at all. >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Thursday, January 08, 2015 2:34 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] recon-all error >>> >>> Hi Mia >>> >>> can you send us the recon-all.log? I don't think you included the >>> error message in your email so there isn't much for us to go on. >>> >>> thanks >>> Bruce >>> >>> On Thu, 8 Jan 2015, Borzello, Mia wrote: >>> >>>> >>>> Hi Freesurfers, >>>> >>>> I'm wondering if you can help with the following error that occurred >>>> when trying to create a reconstruction: >>>> >>>> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 >>>> >>>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >>>> >>>> RedHat release: CentOS release 6.5 (Final) >>>> >>>> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 >>>> >>>> NMR Center info (/space/freesurfer exists): >>>> >>>> machine: huygens >>>> >>>> SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects >>>> >>>> PWD: /autofs/space/huygens_001/users/mia/subjects >>>> >>>> ssh huygens >>>> setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects >>>> cd /autofs/space/huygens_001/users/mia/subjects >>>> >>>> >>>> 1)BI22 >>>> 2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject >>>> BI22_SurferOutput >>>> - >> i/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_B >>>> I19/4571 >>>> /4571157.dcm >>>> 3)recon-all -s exited with ERRORS at Thu Jan 8 13:08:33 EST 2015 >>>> >>>> >>>> Thanks, >>>> m >>>> >>>> >>> >>> ___ >>> 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 > > ___ > 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] Openmp option does not work in Ubuntu 12.04
yes, in 5.3 there is only openmp support in a couple of binaries. Those stages are reached maybe 15 minutes into recon-all depending on your hardware. cheers Bruce On Mon, 12 Jan 2015, Narayanan, Krishnaprasad wrote: Hi Bruce, Thanks for your reply. May be I should not have said it is not working. Sorry for that. The command that I used was "recon-all -i /usr/local/freesurfer/subjects/bert/mri/T1.mgz -subjid exampledata1 -all -openmp 8". Yeah, I observed the core usage using htop until the end of first minute. Until the end of first minute, I saw the CPU utilization only on one of the core and not on all the specified cores. I guess I have found the mistake. The multi core option is enabled only during the mri_em_register_stage and mri_ca_register stage. Can I know approximately at what point in time are these two stages reached? Regards, Krishnaprasad -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Montag, 12. Januar 2015 14:30 To: Freesurfer support list Subject: Re: [Freesurfer] Openmp option does not work in Ubuntu 12.04 Hi Krishnaprasad what is your full recon-all command line? And how do you know it isn't working? Have you tried running "top" during the mri_ca_register stage? The upcoming (one of these months!) release will have much more in the way of openmp optimization cheers Bruce On Mon, 12 Jan 2015, Narayanan, Krishnaprasad wrote: Hallo all, I have installed freesurfer v5.3 on Ubuntu 12.04 LTS. The GCC version is 4.6. I use the recon-all using –all and -openmp option. I observed that openmp does not seem to have any effect in the execution of freesurfer. I verified the installation of openmp using dpkg --status libgomp1 and found that the package was installed. Do I have to install or enable any additional library or flags? Can I kindly get help from the forum to resolve this problem? Best regards, Krishnaprasad ___ 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] Openmp option does not work in Ubuntu 12.04
glad to hear it Bruce On Mon, 12 Jan 2015, Narayanan, Krishnaprasad wrote: Yeah, it works. I am able to see the load on multi cores. Regards, Krishnaprasad -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Montag, 12. Januar 2015 14:51 To: Freesurfer support list Subject: Re: [Freesurfer] Openmp option does not work in Ubuntu 12.04 yes, in 5.3 there is only openmp support in a couple of binaries. Those stages are reached maybe 15 minutes into recon-all depending on your hardware. cheers Bruce On Mon, 12 Jan 2015, Narayanan, Krishnaprasad wrote: Hi Bruce, Thanks for your reply. May be I should not have said it is not working. Sorry for that. The command that I used was "recon-all -i /usr/local/freesurfer/subjects/bert/mri/T1.mgz -subjid exampledata1 -all -openmp 8". Yeah, I observed the core usage using htop until the end of first minute. Until the end of first minute, I saw the CPU utilization only on one of the core and not on all the specified cores. I guess I have found the mistake. The multi core option is enabled only during the mri_em_register_stage and mri_ca_register stage. Can I know approximately at what point in time are these two stages reached? Regards, Krishnaprasad -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Montag, 12. Januar 2015 14:30 To: Freesurfer support list Subject: Re: [Freesurfer] Openmp option does not work in Ubuntu 12.04 Hi Krishnaprasad what is your full recon-all command line? And how do you know it isn't working? Have you tried running "top" during the mri_ca_register stage? The upcoming (one of these months!) release will have much more in the way of openmp optimization cheers Bruce On Mon, 12 Jan 2015, Narayanan, Krishnaprasad wrote: Hallo all, I have installed freesurfer v5.3 on Ubuntu 12.04 LTS. The GCC version is 4.6. I use the recon-all using –all and -openmp option. I observed that openmp does not seem to have any effect in the execution of freesurfer. I verified the installation of openmp using dpkg --status libgomp1 and found that the package was installed. Do I have to install or enable any additional library or flags? Can I kindly get help from the forum to resolve this problem? Best regards, Krishnaprasad ___ 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 ___ 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] make average explanation
Hi Gabriella make_average_subject calls make_average_surface (and make_average_volumes I believe). You probably want to use make_average_subject and let it do what it wants to (that is, let it make everything it knows how to, both surfaces and volumes) cheers Bruce On Mon, 12 Jan 2015, Hirsch, Gabriella wrote: > Hello, > > I am currently trying to visualize group differences in cortical thickness > across subject groups. In addition to using the qdec GUI, I am playing with > the make_average_surface command as well as the make_average_subject command > to then visualize in freeview or tksurfer - though I'm quite sure what the > differences between make_average_surface and make_average_subject are. Can > someone point to any documentation expanding on exactly what these commands > do (differently)? > > Thank you. > Gabriella > > ___ 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 error
Hi Mia you need to run it with the full path of the dicom you are trying to give to recon-all cheers Bruce On Tue, 13 Jan 2015, Borzello, Mia wrote: > Okay, just ran ls-l and don't see it- image attached. > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, January 12, 2015 8:39 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all error > > does that dicom exist? Can you run ls -l on it? > On Sat, 10 Jan 2015, > Borzello, Mia wrote: > >> I just fixed that but I'm still getting an error. I attached a screenshot. >> >> Thanks, >> Mia >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Krieger, Donald N. >> [krieg...@upmc.edu] >> Sent: Friday, January 09, 2015 5:39 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all error >> >> It looks like there's a typo in your recon-all command - there's a space >> between "-" and autorecon3 . >> >> Regards, >> >> Don >> >> >> Don Krieger, Ph.D. >> Department of Neurological Surgery >> University of Pittsburgh >> (412)648-9654 Office >> (412)521-4431 Cell/Text >> >> >>> -Original Message- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- >>> boun...@nmr.mgh.harvard.edu] On Behalf Of Borzello, Mia >>> Sent: Friday, January 09, 2015 5:30 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] recon-all error >>> >>> Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects. >>> I attached the output error for recon-all. >>> >>> Thanks, >>> m >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer- >>> boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Thursday, January 08, 2015 4:27 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] recon-all error >>> >>> did you look in >>> >>> /autofs/space/huygens_001/users/mia/subjects >>> >>> Can you send us the screen output of recon-all? >>> >>> On Thu, 8 Jan 2015, Borzello, >>> Mia wrote: >>> >>>> I looked for that file and did not see a BI22_SurferOutput folder at all. >>>> >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>>> [fis...@nmr.mgh.harvard.edu] >>>> Sent: Thursday, January 08, 2015 2:34 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] recon-all error >>>> >>>> Hi Mia >>>> >>>> can you send us the recon-all.log? I don't think you included the >>>> error message in your email so there isn't much for us to go on. >>>> >>>> thanks >>>> Bruce >>>> >>>> On Thu, 8 Jan 2015, Borzello, Mia wrote: >>>> >>>>> >>>>> Hi Freesurfers, >>>>> >>>>> I'm wondering if you can help with the following error that occurred >>>>> when trying to create a reconstruction: >>>>> >>>>> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 >>>>> >>>>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >>>>> >>>>> RedHat release: CentOS release 6.5 (Final) >>>>> >>>>> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 >>>>> >>>>> NMR Center info (/space/freesurfer exists): >>>>> >>>>> machine: huygens >>>>> >>>>> SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects >>>>> >>>>> PWD: /autofs/space/huygens_001/users/mia/subjects >>>>> >>>>> ssh huygens >>>>> setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects >>>>> cd /autofs/space/huygens_001/users/mia/subjects >>>>> >>>>> >>>>> 1)BI22 >>>>> 2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject >>>>> B
Re: [Freesurfer] recon-all error
Hi Mia you need to give recon-all the name of an actual file. Try that and see if it works cheers Bruce On Tue, 13 Jan 2015, Borzello, Mia wrote: > Hi Bruce, > > Thanks for e-mail. I did a search on the dicom file, and it said there was no > file (top part of image). However, I can get myself in the folder and the > dicome "4571157" is in there. I'm wondering if it's a file type issue. The > files aren't listed as 4571157.dcm for example- could that be the problem? > > Thanks so much, > m > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, January 12, 2015 9:08 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all error > > Hi Mia > > you need to run it with the full path of the dicom you are trying to give > to recon-all > > cheers > Bruce > On Tue, 13 Jan 2015, > Borzello, Mia wrote: > >> Okay, just ran ls-l and don't see it- image attached. >> ____ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Monday, January 12, 2015 8:39 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all error >> >> does that dicom exist? Can you run ls -l on it? >> On Sat, 10 Jan 2015, >> Borzello, Mia wrote: >> >>> I just fixed that but I'm still getting an error. I attached a screenshot. >>> >>> Thanks, >>> Mia >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Krieger, Donald N. >>> [krieg...@upmc.edu] >>> Sent: Friday, January 09, 2015 5:39 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] recon-all error >>> >>> It looks like there's a typo in your recon-all command - there's a space >>> between "-" and autorecon3 . >>> >>> Regards, >>> >>> Don >>> >>> >>> Don Krieger, Ph.D. >>> Department of Neurological Surgery >>> University of Pittsburgh >>> (412)648-9654 Office >>> (412)521-4431 Cell/Text >>> >>> >>>> -Original Message- >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- >>>> boun...@nmr.mgh.harvard.edu] On Behalf Of Borzello, Mia >>>> Sent: Friday, January 09, 2015 5:30 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] recon-all error >>>> >>>> Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects. >>>> I attached the output error for recon-all. >>>> >>>> Thanks, >>>> m >>>> >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer- >>>> boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>>> [fis...@nmr.mgh.harvard.edu] >>>> Sent: Thursday, January 08, 2015 4:27 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] recon-all error >>>> >>>> did you look in >>>> >>>> /autofs/space/huygens_001/users/mia/subjects >>>> >>>> Can you send us the screen output of recon-all? >>>> >>>> On Thu, 8 Jan 2015, Borzello, >>>> Mia wrote: >>>> >>>>> I looked for that file and did not see a BI22_SurferOutput folder at all. >>>>> >>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>>>> [fis...@nmr.mgh.harvard.edu] >>>>> Sent: Thursday, January 08, 2015 2:34 PM >>>>> To: Freesurfer support list >>>>> Subject: Re: [Freesurfer] recon-all error >>>>> >>>>> Hi Mia >>>>> >>>>> can you send us the recon-all.log? I don't think you included the >>>>> error message in your email so there isn't much for us to go on. >>>>> >>>>> thanks >>>>> Bruce >>>>> >>>>> On Thu, 8 Jan 2015, Borzello, Mia wrote: >>>>> >>>>>> >>>>>> Hi Freesurfers
Re: [Freesurfer] missing cortical parcellation labels in aparc+aseg
Hi Peter Christophe Destrieux (ccd) is the creator of this parcellation and is probably the best one to answer. cheers Bruce On Tue, 13 Jan 2015, Peter Smittenaar wrote: Dear Bruce, Mehul and others, The exchange below is from Aug 2014, with Mehul having some missing parcellation labels. I'm facing the same issue with two of my subjects and wonder if Mehul's issue was ever resolved? In my case, using mri_annotation2label on aparc.a2009s returns fewer than 150 labels, with in one case missing lh.G_cingul-Post-ventral.label lh.Lat_Fis-ant-Vertical.label rh.G_cingul-Post-ventral.label and in another lh.S_collat_transv_post rh.S_collat_transv_post My other 22 subjects are fine, recon-all finished without error also in the above 2 subjects, and the Unknown labels do not seem to cover the missing labels. I've tried running recon-all again but no luck. Any thoughts? Many thanks, Peter Mehul Sampat mpsampat at gmail.com Fri Aug 15 22:20:31 EDT 2014 Thank Bruce. I have uploaded the case to transfer/incoming in surfer.nmr.mgh.harvard.edu My file is missingRightParcLabels.tar.gz Mehul On Fri, Aug 15, 2014 at 3:17 PM, Bruce Fischl wrote: > Sure, upload it and one of us will take a look > > Bruce > > On Aug 15, 2014, at 10:28 me PM, Mehul Sampat k wrote: > > Hi Bruce, > rh.aparc.stats looks good and also rh.aparc.a2009s.stats looks correct. > However, both aparc+aseg.mgz and aparc.a2009s+aseg.mgz have the issue with > missing parcellation labels in right hemisphere. > > Also I suspect the issues starts occurring in rh.ribbon.mgz and ribbon.mgz > (missing labels). > (lh.ribbon.mgz is fine) > > I tried to recreate the rh.ribbon.mgz and ribbon.mgz files using the > command below and I am able to reproduce the issue. > mris_volmask <http://freesurfer.net/fswiki/mris_volmask> --label_left_white > 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 > --save_ribbon --save_distance > > I can upload the data if you would like to take a look. > Thanks > Mehul > > > > On Fri, Aug 15, 2014 at 1:54 AM, Bruce Fischl > wrote: > >> How does the rh.aparc look? >> >> On Aug 14, 2014, at 8:13 PM, Mehul Sampat wrote: >> >> Hi Folks, >> We have a strange error for one case. For one case there are missing >> cortical parcellation labels in aparc+aseg.mgz file in the right hemisphere >> (see screenshots) >> >> I looked at the recon-all.log file and no errors are reported. >> Also I recreated aparc+aseg.mgz file using the following command but the >> issue persists: >> mri_aparc2aseg --s subjid --volmask >> I looked at the rh.white and rh.pial and those look good. I cannot figure >> out what would cause such an issue ? I was wondering if anyone has seen >> something similar ? >> Thanks >> Mehul >> >> >> >> >> >> >> >> >> >> >> >> 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 at 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] incomplete preprocessing
Hi Naveed try recon-all -s -make all cheers Bruce On Fri, 16 Jan 2015, Muhammad Naveed Iqbal Qureshi wrote: Hi, How can I execute recon-all on an incomplete preprocessed file in freesurfer. My Pc was accidently shut down during the process. Thank you. Best Regards Naveed ___ 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] Undo manual edits to brainmask.mgz
Hi Kasper yes, this should be doable in matlab. If you erased stuff in the brainmask it should be set to 1 (not 0), so you can find all those voxels, clone the value in from the brain.finalsurfs.mgz, then set them all to 1 in brain.finalsurfs.manedit.mgz cheers Bruce On Thu, 15 Jan 2015, Kasper Jessen wrote: Dear Freesurfer group, I have manual edited, the pial surfaces which extens into the cerebellum, in the brainmask.mgz. I know understand that this should be done in the brain.finalsurfs.manedit.mgz. Is there any way i can "undo" my manuel edits in the brainmask.mgz so i do not need to start over with alle the edits i have done? Best regards, Kasper -- Kasper Jessen, Læge, klinisk assistent Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kaspe...@cnsr.dk eller kasper.jes...@regionh.dk ___ 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] Correcting Pial Surfaces and adding control points at the same time?
Hi Mark yes, that should work cheers Bruce On Thu, 15 Jan 2015, Mark Fletcher wrote: Dear FreeSurfer Community, I am correcting a lot of brains and am wondering if I can combine two steps? Currently, I first correct pial surfaces by manually deleting voxels (dura, bad skull strip, etc). I then run this command. recon-all -autorecon-pial –subjid randomsubject After finishing this, I add control points (often to the temporal lobe) and then run this command recon-all -autorecon2-cp -autorecon3 -subjid randomsubject Although this works, it would save me a lot of time if I could correct the pial surface and control points at the same time? Meaning, I would open the brain once, delete dura that has been traced wrong, add control points (by making a control.dat file in the tmp folder) and then run one code overnight? I am okay if the computer processing takes a bit longer but what is the command (with the correct flags) that I should run? Would it be something like this recon-all -autocron-pial -autorecon2-cp -autorecon3 -subjid randomsubject?? Thanks for your help in advance. -Mark Fletcher UIUC ___ 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] Freesurfer Calculation of Vertex-Wise Area
Hi Bronwyn the surface area at each vertex (I assume you mean vertex and not voxel) is simply the average of the area of the triangles it is attached to. cheers Bruce On Fri, 16 Jan 2015, Bronwyn Overs wrote: > Dear Mailing List, > > I would like to understand how freesurfer calculates the surface area at each > voxel to be used in the GLM procedure. Is there a key methods paper that > describes this process, and can this method be explained in simple terms? > ___ 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] Problem with a recon edit
Hi Celine hard to tell from the slices. Are there voxels labeled ventricle there? If so, you need to correct the aseg. If not, it's probably a topological defect that is fixed incorrectly. If you upload the subject we'll take a look Bruce On Fri, 16 Jan 2015, Celine Louapre wrote: > Sorry forgot the attachement :-) > >> Hi Freesurfer team >> We have been struggling with editing recon for one patient, see the 2 >> slices attached. The problem is that the surface don't go all the way up >> to the bottom of the sulci. I had this some times before but usually >> managed to fix it with editing the wm and the aseg, but this time I >> couldn't have it work correctly. Would you have a clue to help me on that? >> I can put the data in some folders if you want to take a look at the >> entire volumes. >> Thanks for your help >> Celine >> >> -- >> Celine Louapre, MD-PhD >> Research Fellow at Massachusetts General Hospital >> Department of Radiology, MGH >> >> Building 149, Room 2301 >> 13th Street >> Charlestown, MA 02129 >> ___ >> 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] Convert volume index to vertex number in surface
Hi Meiling to go from volume points to the surface you pretty much have to search. We speed this up internally by compiling the surface into a spatial lookup table then only searching through the vertices that are in each bin, but there is no easy external interface to that code (although you are welcome to write such a thing). cheers Bruce On Sat, 17 Jan 2015, Meiling Li wrote: hello I have some points defined in volume (RAS coordination) and now I want to see these locations (vertex number) on surface. I don't know how to do it. I can see one point using tkmedit, input the coordination and save point and then in tksurfer, go to saved point, so I can get the vertex number. However, now i have so many subjects, and so many points defined in volume, how can i find these vertex numbers soon? Thanks in advance! Meiling ___ 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] Creating a .gca file
Hi Pradeep pbsubmit is a wrapper script for submitting a job to a PBS cluster. If you don't have a cluster you should just run the commands that it runs. cheers Bruce On Mon, 19 Jan 2015, pradeep mahato wrote: > Hello experts, > I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I am trying to > create a atlas using previous registered subjects. > It does not complete the mri_ca_normalize phase and stops there. It shows > pbsubmit: Command not found as error. > > Please correct me. Also attaching the rebuild_gca_atlas file. > > Thanks > > Pradeep Kumar Mahato > > ___ 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] converting .nii to .mgz
Hi Mia If all you want to do is convert try mri_convert ct.anat.nii ct.anat.mgz Cheers Bruce > On Jan 19, 2015, at 10:33 PM, Borzello, Mia wrote: > > Hi Freesurfers, > > I'm looking at Freesurfer files from are from years ago trying to look at the > ct.anat file. Unfortunately, i have the nifti file and not the mgz file, so > I'm wondering if there is a way to create it. In trying to find an answer > online, I found this: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html > I tried that but got an error. It may be a syntax error; this was my command > line: recon-all -i > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > MG17_SurferOutput > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > > > FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > > RedHat release: CentOS release 6.5 (Final) > > Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 > > NMR Center info (/space/freesurfer exists): > > machine: huygens > > SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects > > PWD: /autofs/space/huygens_001/users/mia/subjects > > ssh huygens > setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects > cd /autofs/space/huygens_001/users/mia/subjects > > > 1) MG17 > 2) recon-all -i > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > MG17_SurferOutput > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > 3) ERROR: Flag > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > unrecognized. > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > MG17_SurferOutput > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 > x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s exited with ERRORS at Mon Jan 19 22:27:18 EST 2015 > > For more details, see the log file > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > Thanks so much, > Mia > ___ > 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] converting .nii to .mgz
Hi Mia can you please send us the full command line? And also do an ls -l of that file and include it? thanks Bruce On Tue, 20 Jan 2015, Borzello, Mia wrote: > Hi Bruce, > > Thanks for getting back to me so quickly! > I just tried that and got the following error: > reading from ct.anat.nii... > niiRead(): error opening file > /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii > > I'm wondering if the nifti file is possibly corrupted. Is there a way to > check this? > > Thanks so much, > Mia > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, January 19, 2015 10:38 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] converting .nii to .mgz > > Hi Mia > If all you want to do is convert try > > mri_convert ct.anat.nii ct.anat.mgz > > Cheers > Bruce > > > >> On Jan 19, 2015, at 10:33 PM, Borzello, Mia wrote: >> >> Hi Freesurfers, >> >> I'm looking at Freesurfer files from are from years ago trying to look at >> the ct.anat file. Unfortunately, i have the nifti file and not the mgz file, >> so I'm wondering if there is a way to create it. In trying to find an answer >> online, I found this: >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html >> I tried that but got an error. It may be a syntax error; this was my command >> line: recon-all -i >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii >> MG17_SurferOutput >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ >> >> >> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 >> >> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >> >> RedHat release: CentOS release 6.5 (Final) >> >> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 >> >> NMR Center info (/space/freesurfer exists): >> >> machine: huygens >> >> SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects >> >> PWD: /autofs/space/huygens_001/users/mia/subjects >> >> ssh huygens >> setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects >> cd /autofs/space/huygens_001/users/mia/subjects >> >> >> 1) MG17 >> 2) recon-all -i >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii >> MG17_SurferOutput >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ >> 3) ERROR: Flag >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii >> unrecognized. >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii >> MG17_SurferOutput >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ >> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 >> x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s exited with ERRORS at Mon Jan 19 22:27:18 EST 2015 >> >> For more details, see the log file >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> Thanks so much, >> Mia >> ___ >> 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 > > ___ > 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] recon-all on group
Hi Muhammad can you really run 40 subjects at the same time? Usually that means you have a processor farm and it has some mechanism for submitting jobs and load balancing and such (like qsub). cheers Bruce On Tue, 20 Jan 2015, Muhammad Naveed Iqbal Qureshi wrote: Can we apply recon-all on a group of subjects simultaneously? My system has good enough processing power to preprocess 40 subjects at a time, but I have to open 40 terminal windows for doing it now. I need an efficient way to do it. Any suggestions? Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to ___ 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] Viewing QDEC results in tksurfer
Hi Amanda, click the "truncate" button. cheers Bruce On Tue, 20 Jan 2015, Worker, Amanda wrote: > My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh inflate" > d- which is when I got the error. > > I have now tried loading fsaverage first with "tksurfer fsaverage lh > inflated" and it seems to be working fine. > > The problem now is changing the colour scale to display only positive values. > I have played around with the Min, Max and Slope and can't seem to remove > values below zero. What I'm after is a scale showing thickness in mm ranging > from something like 1mm-3.5mm (or if it's easier whatever the min and max > thickness' are for the group) > > Best wishes, > > Amanda > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N Greve > > Sent: 16 January 2015 19:52 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > > what is your command line? > > On 01/16/2015 11:02 AM, Worker, Amanda wrote: >> Hi Doug, >> >> I have set up and run the usual Group Analysis through the command line. I >> have then run " mri_concat output-of-preproc.mgh --mean --o >> mean.output-of-preproc.mgh" to obtain a mean thickness for all subjects >> included in the preprocessing. >> >> I'm now having a problem with visualising this with tksurfer, getting >> ERROR: could not read header info from T1 or orig in >> /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri >> >> Presumably this is because all of the T1/orig are stored in each subjects >> data file and I'm not trying to look at a specific subject. Is there a way >> to get around this problem? >> >> Best wishes, >> >> Amanda >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Douglas N Greve >> >> Sent: 15 January 2015 16:56 >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer >> >> QDEC will not produce mean maps for each group. If this is something you >> want to do, you will need to do it in the command-line group analysis >> stream. See >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >> >> >> >> >> On 01/15/2015 05:25 AM, Worker, Amanda wrote: >>> Hi, >>> >>> I am currently only able to open a thickness map for a single subject using >>> "tksurfer SUBJECT lh inflated". I can use the analysis figures from qdec, >>> but I'd really like to plot the mean thickness for a particular group to >>> compare to others visually. Is this possible? >>> >>> Thanks, >>> >>> Amanda >>> >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> on behalf of Douglas N Greve >>> >>> Sent: 14 January 2015 23:46 >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer >>> >>> what is your tksurfer command line? >>> >>> On 01/13/2015 07:12 AM, Worker, Amanda wrote: Hi, Is it possible to view the results of a qdec analysis (correlation with a single continuous group) in tksurfer? I am currently unable to open it and I'm getting an error saying "could not open file */mri/transforms/talairach.xfm ..no such file or directory" . Is this a file that is not created with qdec? I'm also trying to visualise group mean thickness' in different colours to allow difference between groups, that are not significant in the analysis to be visualised. I cannot find any advice on how to do this, is this something it's possible to do using either freeview of tksurfer? Thanks, Amanda ___ 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. >>> >>> >>>
Re: [Freesurfer] 2D representation of the cortex to get cortical thickness measure
Hi Mohammad, the thickness can be displayed as a map on any surface we create. We do create ?h.sphere files by default, so you can use those if you want. If you'd rather a planar representation you need to make cuts in the inflated surface and use mris_flatten. cheers Bruce On Wed, 21 Jan 2015, Zia, Mohammad wrote: Hi, Is it possible to get over some 2D representation of the cortex (whether it's on a plane, on the surface of a sphere, it doesn't matter (although the plane would probably be easiest to work with)) to get cortical thickness measures at every location? Thanks, --Mohammad This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original. ___ 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_cnr and bash
Hi Jacek if you give us an example of what the desired output would be for you it would just be a couple of minutes to put it in the code. Or maybe someone can post some sed code (or some easy alternative) to parse the CNR out of the output. Bruce On Wed, 21 Jan 2015, Jacek Manko wrote: Oh, I thought it was already defined. I am referring actually to this thread... https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html ...and, allowing myself to specify my problem, when I type the command 'mri_cnr' what I become in my terminal is something more or less like that: " > mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz > processing MRI volume /homes/4/fischl/local_subjects/bruce/mri/norm.mgz... > white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2 > gray/white CNR = 2.241, gray/csf CNR = 1.026 > lh CNR = 1.633 > white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4 > gray/white CNR = 2.205, gray/csf CNR = 0.937 > rh CNR = 1.571 > total CNR = 1.602 " My question is, if there is a way to export the CNR value, that is 1.602, to a seperate file alongside with the subject's ID. I suppose there are no such bulit-in commands in FreeSurfer, is that right? Thanks. Cheers, Jacek Manko Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a): how do you want to define CNR? On 01/21/2015 06:21 AM, Jacek Manko wrote: Dear All, I have been wondering if there is a way (already implemented in the FreeSurfer) to export CNR measurement outputs to seperate file, like a table or someting. If not, it will possible only via some pretty advanced bash scripting, am I right? If so, has anyone some experience with that matter? Thanks. Cheers, Jacek Manko ___ 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 ___ 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_cnr and bash
actually if you run mri_cnr with -l out.log it will write a line to out.log of the form: gray_white_cnr gray_csf_cnr white_mean gray_mean csf_mean sqrt(white_var) sqrt(gray_var) sqrt(csf_var)) so you would create one file for each subject. You could then run a for loop over your subjects to cat them into a single file cheers Bruce On Wed, 21 Jan 2015, Jacek Manko wrote: My desirable output would be then a .txt file that consists of merely two columns. The first column is the subject's ID and the second is the CNR value only, for example: bruce 1.602 bert 1.555 john_doe 1.666 Thanks in advance. Cheers, Jacek Dnia 21-01-2015 o godz. 20:34 Bruce Fischl napisał(a): Hi Jacek if you give us an example of what the desired output would be for you it would just be a couple of minutes to put it in the code. Or maybe someone can post some sed code (or some easy alternative) to parse the CNR out of the output. Bruce On Wed, 21 Jan 2015, Jacek Manko wrote: Oh, I thought it was already defined. I am referring actually to this thread... https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html ...and, allowing myself to specify my problem, when I type the command 'mri_cnr' what I become in my terminal is something more or less like that: " mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz processing MRI volume /homes/4/fischl/local_subjects/bruce/mri/norm.mgz... white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2 gray/white CNR = 2.241, gray/csf CNR = 1.026 lh CNR = 1.633 white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4 gray/white CNR = 2.205, gray/csf CNR = 0.937 rh CNR = 1.571 total CNR = 1.602 " My question is, if there is a way to export the CNR value, that is 1.602, to a seperate file alongside with the subject's ID. I suppose there are no such bulit-in commands in FreeSurfer, is that right? Thanks. Cheers, Jacek Manko Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a): how do you want to define CNR? On 01/21/2015 06:21 AM, Jacek Manko wrote: Dear All, I have been wondering if there is a way (already implemented in the FreeSurfer) to export CNR measurement outputs to seperate file, like a table or someting. If not, it will possible only via some pretty advanced bash scripting, am I right? If so, has anyone some experience with that matter? Thanks. Cheers, Jacek Manko ___ 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 ___ 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] error message recon-all
Hi Lars you have to give recon-all some directive telling it what to do (-all, -autorecon1, -autorecon2, -autorecon3). cheers Bruce On Thu, 22 Jan 2015, Lars M. Rimol wrote: Hi, I keep getting this error message when running, or trying to run, recon-all. I suspect there is a file somewhere indicating that this subject has been run before. But all that is in the directory 3002 is dicom images. What is wrong? [LMR in subjects/DTI ] recon-all -subjid 3002 -i 3002/1.dcm ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. [LMR in subjects/DTI ] recon-all -subjid 3002 ERROR: nothing to do [LMR in subjects/DTI ] ls 3002 100.dcm 107.dcm 113.dcm 11.dcm 126.dcm 132.dcm 139.dcm 145.dcm 151.dcm 158.dcm 19.dcm 25.dcm 31.dcm 38.dcm 44.dcm 50.dcm 57.dcm 63.dcm 6.dcm 76.dcm 82.dcm 89.dcm 95.dcm 101.dcm 108.dcm 114.dcm 120.dcm 127.dcm 133.dcm 13.dcm 146.dcm 152.dcm 159.dcm 1.dcm 26.dcm 32.dcm 39.dcm 45.dcm 51.dcm 58.dcm 64.dcm 70.dcm 77.dcm 83.dcm 8.dcm 96.dcm 102.dcm 109.dcm 115.dcm 121.dcm 128.dcm 134.dcm 140.dcm 147.dcm 153.dcm 15.dcm 20.dcm 27.dcm 33.dcm 3.dcm 46.dcm 52.dcm 59.dcm 65.dcm 71.dcm 78.dcm 84.dcm 90.dcm 97.dcm 103.dcm 10.dcm 116.dcm 122.dcm 129.dcm 135.dcm 141.dcm 148.dcm 154.dcm 160.dcm 21.dcm 28.dcm 34.dcm 40.dcm 47.dcm 53.dcm 5.dcm 66.dcm 72.dcm 79.dcm 85.dcm 91.dcm 98.dcm 104.dcm 110.dcm 117.dcm 123.dcm 12.dcm 136.dcm 142.dcm 149.dcm 155.dcm 16.dcm 22.dcm 29.dcm 35.dcm 41.dcm 48.dcm 54.dcm 60.dcm 67.dcm 73.dcm 7.dcm 86.dcm 92.dcm 99.dcm 105.dcm 111.dcm 118.dcm 124.dcm 130.dcm 137.dcm 143.dcm 14.dcm 156.dcm 17.dcm 23.dcm 2.dcm 36.dcm 42.dcm 49.dcm 55.dcm 61.dcm 68.dcm 74.dcm 80.dcm 87.dcm 93.dcm 9.dcm 106.dcm 112.dcm 119.dcm 125.dcm 131.dcm 138.dcm 144.dcm 150.dcm 157.dcm 18.dcm 24.dcm 30.dcm 37.dcm 43.dcm 4.dcm 56.dcm 62.dcm 69.dcm 75.dcm 81.dcm 88.dcm 94.dcm yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway ___ 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] How to split frames from .mhg files?
Hi Ray this should do the trick: mri_convert -nth 10 all_frames.mgz frame10.mgz or mri_convert all_frames.mgz#10 frame10.mgz note that the second syntax should be accepted by most of our tools cheers Bruce On Thu, 22 Jan 2015, Ray Razlighi wrote: Dear FreeSurfer Experts, I have a .mgh file which contains thickness data for 200 subjects in fsaverage space, so it has 200 frames. When I convert this file to ascii format it only converts the first frame. So I either need to split the .mgh file to single frame files and then convert to ascii or I need the command that converts all the frames into a ascii file/s. Is there any utility in FreeSurfer package that does either of them? Thanks a lot for your help. -- Sincerely, Ray ___ 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_cnr and bash
gray/white CNR is the first column
On Thu, 22 Jan 2015, Jacek Manko wrote:
Dear Dr. Greve, dear Dr. Fischl
would something like this work?
set cnr = `mri_cnr $SUBJECTS_DIR/$subject/surf
$SUBJECTS_DIR/$subject/mri/norm.mgz | grep total | awk '{print $4}'`
echo $subject $cnr > yourfile
Unfortunately it doesnt. I was trying to modify the paths, but got always
results like:
MRISread(/surf/lh.white): could not open file
No such file or directory
mri_cnr: could not read surface file /surf/lh.white
No such file or directory
and @Dr. Fischl
actually if you run mri_cnr with -l out.log it will write a line to
out.log
of the form:
gray_white_cnr gray_csf_cnr white_mean gray_mean csf_mean
sqrt(white_var) sqrt(gray_var) sqrt(csf_var))
so you would create one file for each subject. You could then run a for
loop over your subjects to cat them into a single file
Indeed, but I dont quite get it, how to extract CNR from these values.
Thanks,
Cheers,
Jacek Manko
On 01/21/2015 02:46 PM, Jacek Manko wrote:
My desirable output would be then a .txt file that consists of merely
two columns. The first column is the subject's ID and the second is the
CNR value only, for example:
bruce 1.602
bert 1.555
john_doe 1.666
Thanks in advance.
Cheers,
Jacek
Dnia 21-01-2015 o godz. 20:34 Bruce Fischl napisał(a):
Hi Jacek
if you give us an example of what the desired output would be for you it
would just be a couple of minutes to put it in the code. Or maybe someone
can post some sed code (or some easy alternative) to parse the CNR out of
the output.
Bruce
On Wed,
21 Jan 2015, Jacek Manko wrote:
Oh, I thought it was already defined. I am referring actually to this
thread...
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html
...and, allowing myself to specify my problem, when I type the command
'mri_cnr' what I become in my terminal is something more or less like
that:
"
mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz
processing MRI volume
/homes/4/fischl/local_subjects/bruce/mri/norm.mgz...
white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2
gray/white CNR = 2.241, gray/csf CNR = 1.026
lh CNR = 1.633
white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4
gray/white CNR = 2.205, gray/csf CNR = 0.937
rh CNR = 1.571
total CNR = 1.602
"
My question is, if there is a way to export the CNR value, that is
1.602, to a seperate file alongside with the subject's ID. I suppose
there are no such bulit-in commands in FreeSurfer, is that right?
Thanks.
Cheers,
Jacek Manko
Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a):
how do you want to define CNR?
On 01/21/2015 06:21 AM, Jacek Manko wrote:
Dear All,
I have been wondering if there is a way (already implemented in the
FreeSurfer) to export CNR measurement outputs to seperate file, like a
table or someting. If not, it will possible only via some pretty
advanced bash scripting, am I right? If so, has anyone some experience
with that matter?
Thanks.
Cheers,
Jacek Manko
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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
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The information in this e-mail is intended only for the person to whom
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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
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but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
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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/
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Re: [Freesurfer] automatic reconstruction of abnormal brains
Hi Maria it's really hard to say - you'll need to try it out. There aren't strong prior constraints on skull shape, but if the shape of the brain is too different, things may degrade Bruce On Fri, 23 Jan 2015, Maria Holland wrote: Hi all, I am starting a project analyzing patients with cranial deformities. How robust is the automatic cortical reconstruction process - i.e., would it be able to handle deformed skulls? Similar to this picture: http://upload.wikimedia.org/wikipedia/commons/1/1f/Single_suture_synostosis .png I am also wondering about the possibility of getting information about the intermediate steps of the local gyrification calculation. Like, could we get information on the pial and outer pial surface paths on each individual slice, before that information is turned into a 3D surface? Thanks for your help! ~ Maria ___ 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] Converting dicom images to nifti
have you tried dcmdjpeg or dcmdjpls to uncompress them, then used some other unpacker/converter (mri_convert etc...) cheers Bruce On Tue, 27 Jan 2015, pradeep mahato wrote: > > Please tell how to use dcmunpack. Any help converting dicom to nii. > > On Jan 27, 2015 9:03 PM, "Douglas Greve" wrote: > > Hi Pradeep, I don't think that we can convert that either. > Sorry. > doug > > On 1/27/15 7:18 AM, pradeep mahato wrote: > Hi experts, > > I am trying to convert dicom images namely > 00A0,00A1,00A2 [ No file extension ] etc. These are > generated by Philips machine. I used dcm2nii, it does not give > correct result. It gives warning : this software will only > convert the first slice of this multislice lossless compressed > JPEG . In one thread I read that dicom images from Philips > scanner are oriented differently. > > I tried to use dcmunpack method, but I am not able to save the > converted image. > I used dcmunpack -src . Please share the correct > procedure. > > In one of the subjects I have very less number of images:30. Is > it necessary to have more dicom images to have a better brain > mri image . If yes, what should be the optimal number of images > > Thanking You > > Pradeep Kumar Mahato > > > ___ > 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
Re: [Freesurfer] Converting dicom images to nifti
p.s. sorry, I missed the multiframe part. I guess dcmunpack and mri_convert won't work, but maybe decompressing and using something else afterwards will do the trick? On Tue, 27 Jan 2015, Douglas Greve wrote: > If you run it with --help there will be lots of documentation and examples. > It will not be able to convert the multiframe dicom files though > > On 1/27/15 12:24 PM, pradeep mahato wrote: > > Please tell how to use dcmunpack. Any help converting dicom to > nii. > > On Jan 27, 2015 9:03 PM, "Douglas Greve" >wrote: > > Hi Pradeep, I don't think that we can convert that > either. Sorry. > doug > > On 1/27/15 7:18 AM, pradeep mahato wrote: > Hi experts, > > I am trying to convert dicom images namely > 00A0,00A1,00A2 [ No file extension ] etc. > These are generated by Philips machine. I used dcm2nii, it > does not give correct result. It gives warning : this > software will only convert the first slice of this > multislice lossless compressed JPEG . In one thread I read > that dicom images from Philips scanner are oriented > differently. > > I tried to use dcmunpack method, but I am not able to save > the converted image. > I used dcmunpack -src . Please share the correct > procedure. > > In one of the subjects I have very less number of > images:30. Is it necessary to have more dicom images to > have a better brain mri image . If yes, what should be the > optimal number of images > > Thanking You > > Pradeep Kumar Mahato > > > ___ > 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
Re: [Freesurfer] eTIV correction and registration in common space
Hi Steano a) You could do this but then you are testing a somewhat different hypothesis - that the change in a specific structure is more than the overall change in gray matter. Thus for example, widespread atrophy would be regressed out. If that's what you are interested in, then this approach is fine. b) Our analysis is always in individual subject space. You can transform to a common space using mri_vol2vol if you want. cheers Bruce On Tue, 27 Jan 2015, std...@virgilio.it wrote: Hi list, please, I have two questions: a) subcortical volume correction in cross-sectional studies could be done by using total GM as covariate instead of eTIV? b) relatively to group subcortical analysis in cross-sectional studies, the anatomical images should be necessarily transformed in common space or is possible to perform the analysis in native space? The registration in common space should minimize issues due to different head size. The computation on native space could bias the results considering the different head sizes among subjects? Thanks, Stefano ___ 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] pial extends to cerebellum even after edits
Hi Sneha can you send us some snapshots? Or upload the entire subject and we will take a look. You can always erase cerebellum from brain.finalsurfs and rerun recon3 cheers Bruce On Wed, 28 Jan 2015, Sneha Pandya wrote: > Hi Team, > > Can anyone please share if they have been successful in editing extending > pial to the cerebellum and which method has been successful in reference to > the email below. > > Thanks, > Sneha > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sneha Pandya > [snp2...@med.cornell.edu] > Sent: Tuesday, January 27, 2015 12:03 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Which command to use if pial extends to cerebellum > > Hi Team, > > I have few of my images in which pial surface extends to the cerebellum. > Please note that I have already made edits to the brainmask.mgz and have > already ran following command: > > recon-all -autorecon-pial -subjid subj > After lookin into several previous posts and freesurfer edit forum I came > across following solutions but its not clear which one to use when. Can > someone please shed a light to which recon command be used post making edits > to brain.finalsurfs.manedit.mgz for cerebellum and pial edits to > brainmask.mgz. I have also attached a screenshot for one of my case. > > recon-all -autorecon-pial -autorecon3 -subjid subj > OR > recon-all -make all -s subjid > OR > recon-all -all -clean-bm -s subjid > Thanks, > Sneha > > ___ 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] Volumes differ in geometry
Hi Yawu Can you upload those two volumes so we can take a look? Cheers Bruce > On Jan 28, 2015, at 4:33 PM, Liu Y wrote: > > Dear experts, > Recently I run freesurfer longitudinal analysis > (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0), during the creation of > the BASE, I get the following error "Volumes differ in geometry row=1 col=4 > diff=4.745766(4.74577)". We did not change the protocol during the study > period. I check the baseline and follow-up images with mri_info, it shows > like this for baseline images . > Volume information for K_EL03_1.nii.gz > type: nii > dimensions: 208 x 256 x 160 > voxel sizes: 1.1719, 1.1719, 1.2000 > type: FLOAT (3) > fov: 243.750 > dof: 0 > xstart: -121.9, xend: 121.9 > ystart: -150.0, yend: 150.0 > zstart: -96.0, zend: 96.0 > TR: 2400.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees > nframes: 1 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = 0., y_r = 0., z_r = 1., c_r = 1.9559 > : x_a = -1., y_a = 0., z_a = 0., c_a =24.3864 > : x_s = 0., y_s = 1., z_s = 0., c_s = -21.0540 > Orientation : PSR > Primary Slice Direction: sagittal > > voxel to ras transform: > 0. 0. 1.2000 -94.0441 > -1.1719 0. 0. 146.2614 > 0. 1.1719 0. -171.0540 > 0. 0. 0. 1. > > voxel-to-ras determinant -1.64795 > ras to voxel transform: > -0. -0.8533 -0. 124.809 -0. -0. 0.8533 145.9661 > 0.8333 0. 0.78.3701 > 0. 0. 0. 1. > > > and for followup images:Volume information for K_EL03_2.nii.gz > type: nii > dimensions: 208 x 256 x 160 > voxel sizes: 1.1719, 1.1719, 1.2000 > type: FLOAT (3) > fov: 243.750 > dof: 0 > xstart: -121.9, xend: 121.9 > ystart: -150.0, yend: 150.0 > zstart: -96.0, zend: 96.0 > TR: 2400.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees > nframes: 1 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = 0., y_r = 0., z_r = 1., c_r =-2.7898 > : x_a = -1., y_a = 0., z_a = 0., c_a =17.2881 > : x_s = 0., y_s = 1., z_s = 0., c_s = -34.7603 > Orientation : PSR > Primary Slice Direction: sagittal > > voxel to ras transform: > 0. 0. 1.2000 -98.7898 > -1.1719 0. 0. 139.1631 > 0. 1.1719 0. -184.7603 > 0. 0. 0. 1. > > voxel-to-ras determinant -1.64795 > > ras to voxel transform: > -0. -0.8533 -0. 118.7526 > -0. -0. 0.8533 157.6622 > 0.8333 0. 0.82.3249 > 0. 0. 0. 1. > > I have no ideal what is going wrong. Please help. > By the way I used dcm2nii Gui (compressed FSL 4DNIfTInii) convert dcm to > nii.gz. > Thanks, > > Yawu > > ___ > 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] Volumes differ in geometry
Hi Yawu what was the freesurfer command you ran that gave you the error? Can you send us the command and the full screen output? thanks Bruce On Thu, 29 Jan 2015, Liu Y wrote: Hi Bruce, I have uploaded the baseline K_EL03_1.nii.gz and followup K_EL03_2.nii.gz via FTP File Exchange. Thanks, Yawu On Thu, Jan 29, 2015 at 3:28 AM, Bruce Fischl wrote: Hi Yawu Can you upload those two volumes so we can take a look? Cheers Bruce On Jan 28, 2015, at 4:33 PM, Liu Y wrote: Dear experts, Recently I run freesurfer longitudinal analysis (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0), during the creation of the BASE, I get the following error "Volumes differ in geometry row=1 col=4 diff=4.745766(4.74577)". We did not change the protocol during the study period. I check the baseline and follow-up images with mri_info, it shows like this for baseline images . Volume information for K_EL03_1.nii.gz type: nii dimensions: 208 x 256 x 160 voxel sizes: 1.1719, 1.1719, 1.2000 type: FLOAT (3) fov: 243.750 dof: 0 xstart: -121.9, xend: 121.9 ystart: -150.0, yend: 150.0 zstart: -96.0, zend: 96.0 TR: 2400.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0., y_r = 0., z_r = 1., c_r = 1.9559 : x_a = -1., y_a = 0., z_a = 0., c_a =24.3864 : x_s = 0., y_s = 1., z_s = 0., c_s = -21.0540 Orientation : PSR Primary Slice Direction: sagittal voxel to ras transform: 0. 0. 1.2000 -94.0441 -1.1719 0. 0. 146.2614 0. 1.1719 0. -171.0540 0. 0. 0. 1. voxel-to-ras determinant -1.64795 ras to voxel transform: -0. -0.8533 -0. 124.809 -0. -0. 0.8533 145.9661 0.8333 0. 0.78.3701 0. 0. 0. 1. > and for followup images:Volume information for K_EL03_2.nii.gz type: nii dimensions: 208 x 256 x 160 voxel sizes: 1.1719, 1.1719, 1.2000 type: FLOAT (3) fov: 243.750 dof: 0 xstart: -121.9, xend: 121.9 ystart: -150.0, yend: 150.0 zstart: -96.0, zend: 96.0 TR: 2400.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0., y_r = 0., z_r = 1., c_r = -2.7898 : x_a = -1., y_a = 0., z_a = 0., c_a =17.2881 : x_s = 0., y_s = 1., z_s = 0., c_s = -34.7603 Orientation : PSR Primary Slice Direction: sagittal voxel to ras transform: 0. 0. 1.2000 -98.7898 -1.1719 0. 0. 139.1631 0. 1.1719 0. -184.7603 0. 0. 0. 1. voxel-to-ras determinant -1.64795 ras to voxel transform: -0. -0.8533 -0. 118.7526 -0. -0. 0.8533 157.6622 0.8333 0. 0.82.3249 0. 0. 0. 1. I have no ideal what is going wrong. Please help. By the way I used dcm2nii Gui (compressed FSL 4DNIfTInii) convert dcm to nii.gz. Thanks, Yawu ___ 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] subcortical brain intensity
Hi Rujing it is the mean intensity within the structure from the norm.mgz I believe cheers Bruce On Thu, 29 Jan 2015, Rujing Zha wrote: HI all What is mean of the subcortical intensity in the aseg.stats file? Thanks. rujing ___ 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] MNI305 coordinates to RAS
Hi Juan if you invert that matrix it will go the other direction cheers Bruce On Thu, 29 Jan 2015, Diaz Rodriguez, Juan wrote: I am trying to convert MNI305 coordinates to RAS. I have only been able to find a way to find MNI305 from RAS but not the other way around: MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' from http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystemshttp://surfer.nmr .mgh.harvard.edu/fswiki/CoordinateSystems Is there a known equation with transforms to go from MNI to RAS? Thanks, Juan ___ 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] MNI305 coordinates to RAS
Hi Juan add a 4th row that is [0 0 0 1], then invert it cheers Bruce On Thu, 29 Jan 2015, Diaz Rodriguez, Juan wrote: > Hi Bruce, > > The problem is that it TalXFM is a 3x4 matrix. It needs to be a square matrix > to be inverted. > > Juan > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, January 29, 2015 3:33 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] MNI305 coordinates to RAS > > Hi Juan > > if you invert that matrix it will go the other direction > > cheers > Bruce > On Thu, 29 Jan > 2015, Diaz Rodriguez, Juan wrote: > >> I am trying to convert MNI305 coordinates to RAS. I have only been able to >> find a way to find MNI305 from RAS but not the other way around: >> MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' from >> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystemshttp://surfer.nmr >> .mgh.harvard.edu/fswiki/CoordinateSystems >> >> Is there a known equation with transforms to go from MNI to RAS? >> >> Thanks, >> >> Juan >> >> > > ___ > 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] Volumes differ in geometry
Hi Yawu the recon-all.log indicates that building the base finished without error. What command did you run that gave you the error? The original nifti files will have different geometries since the subject will be in a different location in the scanner, but that should be normalized out by the longitudinal stream. cheers Bruce On Fri, 30 Jan 2015, Liu Y wrote: Hi Bruce,I run the command recon-all -base K_EL03_base -tp K_EL03_1 -tp K_EL03_2 -all.I am to upload the recon_all.log to you. Thanks, Yawu On Thu, Jan 29, 2015 at 6:07 PM, Bruce Fischl wrote: Hi Yawu what was the freesurfer command you ran that gave you the error? Can you send us the command and the full screen output? thanks Bruce On Thu, 29 Jan 2015, Liu Y wrote: Hi Bruce, I have uploaded the baseline K_EL03_1.nii.gz and followup K_EL03_2.nii.gz via FTP File Exchange. Thanks, Yawu On Thu, Jan 29, 2015 at 3:28 AM, Bruce Fischl wrote: Hi Yawu Can you upload those two volumes so we can take a look? Cheers Bruce On Jan 28, 2015, at 4:33 PM, Liu Y wrote: Dear experts, Recently I run freesurfer longitudinal analysis (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0), during the creation of the BASE, I get the following error "Volumes differ in geometry row=1 col=4 diff=4.745766(4.74577)". We did not change the protocol during the study period. I check the baseline and follow-up images with mri_info, it shows like this for baseline images . Volume information for K_EL03_1.nii.gz type: nii dimensions: 208 x 256 x 160 voxel sizes: 1.1719, 1.1719, 1.2000 type: FLOAT (3) fov: 243.750 dof: 0 xstart: -121.9, xend: 121.9 ystart: -150.0, yend: 150.0 zstart: -96.0, zend: 96.0 TR: 2400.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0., y_r = 0., z_r = 1., c_r = 1.9559 : x_a = -1., y_a = 0., z_a = 0., c_a =24.3864 : x_s = 0., y_s = 1., z_s = 0., c_s = -21.0540 Orientation : PSR Primary Slice Direction: sagittal voxel to ras transform: 0. 0. 1.2000 -94.0441 -1.1719 0. 0. 146.2614 0. 1.1719 0. -171.0540 0. 0. 0. 1. voxel-to-ras determinant -1.64795 ras to voxel transform: -0. -0.8533 -0. 124.809 -0. -0. 0.8533 145.9661 0.8333 0. 0.78.3701 0. 0. 0. 1. > and for followup images:Volume information for K_EL03_2.nii.gz type: nii dimensions: 208 x 256 x 160 voxel sizes: 1.1719, 1.1719, 1.2000 type: FLOAT (3) fov: 243.750 dof: 0 xstart: -121.9, xend: 121.9 ystart: -150.0, yend: 150.0 zstart: -96.0, zend: 96.0 TR: 2400.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0., y_r = 0., z_r = 1., c_r = -2.7898 : x_a = -1., y_a = 0., z_a = 0., c_a =17.2881 : x_s = 0., y_s = 1., z_s = 0., c_s = -34.7603 Orientation : PSR Primary Slice Direction: sagittal voxel to ras transform: 0. 0. 1.2000 -98.7898 -1.1719 0. 0. 139.1631 0. 1.1719 0.00
Re: [Freesurfer] subsampling procedure for fsaverages
Hi Ernst The new vertices are added o the end, so all the fsaverage5 vertex numbers should be the same in fsaverage6 Cheers Bruce > On Feb 2, 2015, at 10:33 AM, Ernst Schwartz > wrote: > > Hi! > > I have some data that's on a low-resolution mesh (fsaverage5) that I would > like to upsample to higher resolutions (fsaverage6 and fsaverage), but I > can't figure out the correct vertex numbering. Is there a function that I > could use (in the sense of function_on_fsaverage6 = > peform_subdivision(function_on_fsaverage5) ) or if there isn't, could you > briefly describe how new vertices are added during upsampling (eg. the > ordering of new vertices with respect to the old ones)? > > thanks a lot! > > ~ > > Ernst Schwartz > Computational Image Research (CIR) Lab > Department of Biomedical Imaging and Image-guided Therapy > Medical University Vienna, Austria > > -- > > ___ > 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] Age verification
Hi David this one is a good one to cite: Satrajit S Ghosh, Sita Kakunoori, Jean Augustinack, Alfonso Nieto-Castanon, Ioulia Kovelman, Nadine Gaab, Joanna A Christodoulou, Christina Triantafyllou, John D E Gabrieli, Bruce Fischl (2010) Evaluating the validity of volume-based and surface-based brain image registration for developmental cognitive neuroscience studies in children 4 to 11 years of age. Neuroimage 53: 1. 85-93 Oct. cheers Bruce On Mon, 2 Feb 2015, david.kam...@pet.wayne.edu wrote: > What is the youngest age group the present freesurfer templare has been > validated for? > I?d appreciate (and quote) relevant paper suggestions. > > Thanks, > David > > ___ > 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] Cortical Thickness under iEEG leads
sure, just draw an ROI in the volume (in e.g. freeview) and save it as a .label file, then load it into tksurfer and it will get sampled onto the surface (then save it) On Tue, 3 Feb 2015, rwlod...@uic.edu wrote: > Hello! > I was just wondering what the best way to find the cortical thickness > under specific intracranial EEG leads is. Is this even possible? I know > freesurfer doesn't allow you to place leads onto the 3D model it > generates, but if I knew exactly where the lead was is there some way to > determine the thickness for that small area? Thanks! > > Rich > > ___ > 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] recon-all dimensions
yes it does cheers Bruce On Thu, 5 Feb 2015, jwa...@nmr.mgh.harvard.edu wrote: > Hello Freesurfer, > My MPRAGE dimensions are 1x1x1.33. The output of recon-all appears to > be 1x1x1, judging by the fact that the aseg.stats columns for voxel > number and volume in mm3 are identical. Should I conclude from this > that recon-all resamples the scan into 1x1x1 voxels? > > Thank you, > Jeff > > ___ > 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] Freesurfer could not accurately recognize the voxel size
Hi Yawu what was the full recon-all command line? What is your input format? If all else fails you can mri_convert your input volume nifti or mgz and override what is in the header (e.g. mri_convert -iks 1 ...) cheers Bruce On Fri, 6 Feb 2015, Liu Y wrote: > Dear Experts, > When I run recon-all -cw256 -s problemcase -all, the program seems not able > accurately to recognize the voxel size in this problematic case, in other > cases there is no problem. The program gave a warning like this: > > WARNING=== > == > The physical sizes are (240.00 mm, 240.00 mm, 338.00 mm), which cannot fit > in 256^3 mm^3 volume. > The resulting volume will have 338 slices. > If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). > === > == > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from /usr/local/src/freesurfer/subjects/T8_1/mri/rawavg.mgz... > TR=8.08, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, 1) > k_ras = (1, 0, 0) > Original Data has (1, 1, 2) mm size and (240, 240, 169) voxels. > Data is conformed to 1 mm size and 338 voxels for all directions > changing data type from float to uchar (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing to /usr/local/src/freesurfer/subjects/Turku8_1/mri/orig.mgz... > > > ERROR! FOV=338.000 > 256 > Include the flag -cw256 with recon-all! > Inspect orig.mgz to ensure the head is fully visible. > > > Then I checked the orig.mgz, the image was re-scaled (stretched) in > left-right direction, and could not see the left and right boundaries of the > brain. The program said that the Original Data has (1, 1, 2) mm size, but > actually the voxel size is 1*1*1 mm3. > > The freesurfer version 5.3, Ubuntu 12.04 > > Thanks, > > Yawu > > > > ___ 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] Labeling of preSMA?
Hi Silas as far as I know there isn't a presma label. I'm also not sure how well thresholding based on y will do either. sorry Bruce On Fri, 6 Feb 2015, Silas wrote: > Hi Freesurfer team, > > I'm currently investigating the volume of preSMA. Is there an existing label > of preSMA? > > If not, together preSMA and SMA is also known as Brodmann Area 6, which is > labeled already. PreSMA is located just rostrally to SMA in BA6, and i was > wondering if it is possible to distinguish between preSMA and SMA by making > a limit in y=0? > > Thanks, > > Best, Silas > > ___ 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] Freesurfer could not accurately recognize the voxel size
and what was the recon-all -i command line? Does the rawavg.mgz look correct? You can send us whatever file you gave to recon-all -i and we'll see why it is being converted incorrectly, or you can try the mri_convert command line I gave below (check out mri_convert --help) to override the voxel size info we read out of the header On Fri, 6 Feb 2015, Liu Y wrote: Hi Bruce,The full recon-all command line is "recon-all -cw256 -s T8_1 -all" and the input format is mgz. The mgz file is created by running recon-all -i. The 001.mgz under /mri/orig looks just normal, but when complete the "recon-all -cw256 -s T8_1 -all", the orig.mgz was re-scaled (stretched) in left-right direction, and could not see the left and right boundaries of the brain. Thanks, Yawu On Fri, Feb 6, 2015 at 3:18 PM, Bruce Fischl wrote: Hi Yawu what was the full recon-all command line? What is your input format? If all else fails you can mri_convert your input volume nifti or mgz and override what is in the header (e.g. mri_convert -iks 1 ...) cheers Bruce On Fri, 6 Feb 2015, Liu Y wrote: > Dear Experts, > When I run recon-all -cw256 -s problemcase -all, the program seems not able > accurately to recognize the voxel size in this problematic case, in other > cases there is no problem. The program gave a warning like this: > >WARNING==== === > == > The physical sizes are (240.00 mm, 240.00 mm, 338.00 mm), which cannot fit > in 256^3 mm^3 volume. > The resulting volume will have 338 slices. > If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). >=== > == > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from /usr/local/src/freesurfer/subjects/T8_1/mri/rawavg.mgz... > TR=8.08, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, 1) > k_ras = (1, 0, 0) > Original Data has (1, 1, 2) mm size and (240, 240, 169) voxels. > Data is conformed to 1 mm size and 338 voxels for all directions > changing data type from float to uchar (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing to /usr/local/src/freesurfer/subjects/Turku8_1/mri/orig.mgz... > > > ERROR! FOV=338.000 > 256 > Include the flag -cw256 with recon-all! > Inspect orig.mgz to ensure the head is fully visible. > > > Then I checked the orig.mgz, the image was re-scaled (stretched) in > left-right direction, and could not see the left and right boundaries of the > brain. The program said that the Original Data has (1, 1, 2) mm size, but > actually the voxel size is 1*1*1 mm3. > > The freesurfer version 5.3, Ubuntu 12.04 > > Thanks, > > Yawu > > > > ___ 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] bbregister error [Was: TRACULA mask error]
try --init-spm On Fri, 6 Feb 2015, Anastasia Yendiki wrote: > > Hi Amanda - So it looks like --init-header didn't work, and neither does > --init-fsl. I'll defer to the father of bbregister, Doug, for clues about > how to proceed. > > a.y > > On Wed, 21 Jan 2015, Worker, Amanda wrote: > >> Hi Anastasia, >> >> Yes I have done that. My command line was... " bbregister --s PDPLUS010 >> --init-header --dti --mov >> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/dwi.nii.gz >> --reg >> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/anatorig2diff.bbr.dat >> --fslmat >> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/diff2anatorig.bbr.mat >> " >> >> Following the instructions printed I can only see a tiny bit of the >> dwi.nii.gz, as attached. >> >> I've also tried substituting --dti for --t1 in the command line and that >> doesn't make much difference. >> >> Do you have any other ideas? >> >> Thanks, >> >> Amanda >> >> >> >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Anastasia Yendiki >> >> Sent: 15 January 2015 15:36 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA mask error >> >> Did you follow the instructions and the end of the output of the >> bbregister command? What does that look like? See what I wrote below about >> looking for the bbregister command in trac-all.log, running it separately >> on one subject after changing that one option and looking at its output. >> >> On Wed, 14 Jan 2015, Worker, Amanda wrote: >> >>> Sorry, I misunderstood. >>> >>> I've attached a screenshot of what I can see, it does look like there is >>> probably a different problem now as both the dtifit_FA.nii.gz and >>> aparc+aseg.bbr.nii are completely off centre. >>> >>> Thanks, >>> >>> Amanda >>> >>> >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> on behalf of Anastasia Yendiki >>> >>> Sent: 13 January 2015 17:52 >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] TRACULA mask error >>> >>> It's impossible to know unless you actually check the registration. See my >>> previous email below on how to do that. >>> >>> On Tue, 13 Jan 2015, Worker, Amanda wrote: >>> I have edited the trac-preproc script to "--init-header" instead of "--init-fsl" - hoping that this would fix the registration problem. Perhaps this hasn't helped? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki Sent: 12 January 2015 19:58 To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA mask error Have you checked that the registration has been fixed? It looks like it might not. On Mon, 12 Jan 2015, Worker, Amanda wrote: > Yes of course. Please find attached. > > Thanks, > > Amanda > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Anastasia Yendiki > > Sent: 12 January 2015 16:39 > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA mask error > > Can you please attach the entire trac-all.log file? It's hard to tell just > from the last few lines, the initial error may have happened much earlier. > > On Mon, 12 Jan 2015, Worker, Amanda wrote: > >> Hi Anastasia, >> >> Thank you for your response. I have made the changes that you >> recommended and attempted to run trac-all -prep on one of the subjects >> with errors. I am now getting the following error: >> >> Writing output files to >> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_* >> Writing spline volumes to >> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz >> Segmentation fault >> >> trac-preproc-edit exited with ERRORS at Fri Jan >> >> >> Do you have any idea what the problem could be now? >> >> Thanks, >> >> Amanda >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: 07 January 2015 17:11 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA mask error >> >> Hi Amanda - See attached screenshot of your data, there is a gross >> misregistration (~45 degree angle rotation) between the diffusion and >> anatomical. You can check if this is the case for the rest of your bad >> cases by superimposing the FA map (dmri/dtifit_FA.nii.gz) and anatomical >> segmentation mapped to diffusion space (dlabel/diff/aparc+aseg.bbr.nii). >> >> According to bbregister czar Doug, a big error like this in bbregister >> happ
Re: [Freesurfer] Differing dimensions between curvature and inflated files
Hi Phil try running recon-all -make all on those subjects. Something was rebuilt but not run to completion I suspect. cheers Bruce On Sun, 8 Feb 2015, Kelly, Philip wrote: Dear FreeSurfer experts, I am running Spherical Daemon on my reconstructed surfaces as part of the Winkler et al (2012) method of analysing surface area. The majority of my subject’s surfaces are read perfectly fine, however it exits with error on one particular subject. It seems that the problem is that the curv and sulc files dimensions are different to the inflated file (e.g. 158102x1 vs. 158100x1). This is the case for a handful of my participants. I ran –vno-check on these participants and the number of vertices match for both left and right hemispheres. I have included these participants in cortical thickness analysis using QDEC and I didn’t receive any errors relating to mismatched dimensions (I’m not sure if I would anyway). How would you suggest I proceed so that the curv, sulc and inflated files for these participants are the same and can be inputted into Spherical Daemon? Thank you in advance for any information you may be able to provide on this. All the best, Phil Kelly ___ 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] Freesurfer could not accurately recognize the voxel size
glad to hear it worked out Bruce On Sun, 8 Feb 2015, Liu Y wrote: Hi Douglas and Bruce, Thanks for your suggestions. I found the reason. The mistake begins from the compressing dcm to nii by using dcm2nii. In the first 3 dcm images, two of them have same index, then the dcm2nii could not keep the original information of voxel size. I omitted the first 3 dcm images then it worked during freesurfer analysis. Cheers Yawu On Fri, Feb 6, 2015 at 6:26 PM, Bruce Fischl wrote: and what was the recon-all -i command line? Does the rawavg.mgz look correct? You can send us whatever file you gave to recon-all -i and we'll see why it is being converted incorrectly, or you can try the mri_convert command line I gave below (check out mri_convert --help) to override the voxel size info we read out of the header On Fri, 6 Feb 2015, Liu Y wrote: Hi Bruce,The full recon-all command line is "recon-all -cw256 -s T8_1 -all" and the input format is mgz. The mgz file is created by running recon-all -i. The 001.mgz under /mri/orig looks just normal, but when complete the "recon-all -cw256 -s T8_1 -all", the orig.mgz was re-scaled (stretched) in left-right direction, and could not see the left and right boundaries of the brain. Thanks, Yawu On Fri, Feb 6, 2015 at 3:18 PM, Bruce Fischl wrote: Hi Yawu what was the full recon-all command line? What is your input format? If all else fails you can mri_convert your input volume nifti or mgz and override what is in the header (e.g. mri_convert -iks 1 ...) cheers Bruce On Fri, 6 Feb 2015, Liu Y wrote: > Dear Experts, > When I run recon-all -cw256 -s problemcase -all, the program seems not able > accurately to recognize the voxel size in this problematic case, in other > cases there is no problem. The program gave a warning like this: > >WARNING=== = === > == > The physical sizes are (240.00 mm, 240.00 mm, 338.00 mm), which cannot fit > in 256^3 mm^3 volume. > The resulting volume will have 338 slices. > If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). >== = > == > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from /usr/local/src/freesurfer/subjects/T8_1/mri/rawavg.mgz... > TR=8.08, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, 1) > k_ras = (1, 0, 0) > Original Data has (1, 1, 2) mm size and (240, 240, 169) voxels. > Data is conformed to 1 mm size and 338 voxels for all directions > changing data type from float to uchar (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing to /usr/local/src/freesurfer/subjects/Turku8_1/mri/orig.mgz... > > > ERROR! FOV=338.000 > 256 > Include the flag -cw256 with recon-all! > Inspect orig.mgz to ensure the head is fully visible. > > > Then I checked the orig.mgz, the image was re-scaled (stretched) in > left-right direction, and could not see the left and right boundaries of the > brain. The program said that the Original Data has (1, 1, 2) mm size, but > actually the voxel size is
Re: [Freesurfer] Reduction of image size
mri_extract should do the trick Bruce On Sun, 8 Feb 2015, SOURAV RANJAN KOLE wrote: > Dear Freesurfer community, > Please let me know of an elegant way to reduce image size from 256x256x256 > to 256x256x160 and keeping the voxel size the same. The images are currently > in analyze format but I have access to mri_convert and ImageConvert. > > Thank you. > > Sourav > > ___ 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] Reduction of image size
Hi Sourav mri_extract usage: mri_extract x0 y0 z0 dx dy dz (x0, y0, z0) is the starting coordinate of the rectangle to extract *not* the size. (dx, dy, dz) is the size. Yours should be something like: mri_extract input.mgz 0 0 0 256 256 160 output.mgz or maybe you don't want to start at 0, but further into the volume. Also, definitely do NOT use .img at any point as you will lose direction cosine info cheers Bruce On Sun, 8 Feb 2015, SOURAV RANJAN KOLE wrote: > Hello Bruce, > > Thank you for the prompt reply. > > Although, mri_extract is creating new files but it is giving me the following > error- MRIextractInto: bad src location (256, 256, 160). Also, ITK-SNAP > cannot read the new image file. > > Here is what I am doing: > 1. Converting from .mgz to .img > mri_convert brainmask.mgz brainmask.img --conform --out_data_type float > 2. Reducing size of image > mri_extract brainmask.img 256 256 160 1 1 1 new_brainmask.img > > I would like the new images to be 256x256x160 and voxel size to be 1x1x1. Am > I not using mri_extract correctly? > > Thank you. > > Regards, > > Sourav > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Sunday, February 08, 2015 4:12 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Reduction of image size > > mri_extract should do the trick > Bruce > On Sun, 8 Feb 2015, SOURAV RANJAN KOLE > wrote: > >> Dear Freesurfer community, >> Please let me know of an elegant way to reduce image size from 256x256x256 >> to 256x256x160 and keeping the voxel size the same. The images are currently >> in analyze format but I have access to mri_convert and ImageConvert. >> >> Thank you. >> >> Sourav >> >> > ___ > 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
Re: [Freesurfer] Reduction of image size
Hi Sourav Can you explain why you are reslicing? Cheers Bruce > On Feb 8, 2015, at 7:26 PM, SOURAV RANJAN KOLE wrote: > > Thank you, again, Bruce. > > How do I determine the starting coordinates for extraction, so I do not > cutoff relevant info? > > Regards, > > Sourav > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Sunday, February 08, 2015 5:04 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Reduction of image size > > Hi Sourav > > mri_extract > usage: mri_extract x0 y0 z0 dx dy dz > > (x0, y0, z0) is the starting coordinate of the rectangle to extract *not* > the size. (dx, dy, dz) is the size. Yours should be something like: > > mri_extract input.mgz 0 0 0 256 256 160 output.mgz > > > or maybe you don't want to start at 0, but further into the volume. > > Also, definitely do NOT use .img at any point as you will lose direction > cosine info > > cheers > Bruce > > On Sun, > 8 Feb 2015, SOURAV RANJAN KOLE wrote: > >> Hello Bruce, >> >> Thank you for the prompt reply. >> >> Although, mri_extract is creating new files but it is giving me the >> following error- MRIextractInto: bad src location (256, 256, 160). Also, >> ITK-SNAP cannot read the new image file. >> >> Here is what I am doing: >> 1. Converting from .mgz to .img >> mri_convert brainmask.mgz brainmask.img --conform --out_data_type float >> 2. Reducing size of image >> mri_extract brainmask.img 256 256 160 1 1 1 new_brainmask.img >> >> I would like the new images to be 256x256x160 and voxel size to be 1x1x1. Am >> I not using mri_extract correctly? >> >> Thank you. >> >> Regards, >> >> Sourav >> >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Sunday, February 08, 2015 4:12 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Reduction of image size >> >> mri_extract should do the trick >> Bruce >> On Sun, 8 Feb 2015, SOURAV RANJAN KOLE >> wrote: >> >>> Dear Freesurfer community, >>> Please let me know of an elegant way to reduce image size from 256x256x256 >>> to 256x256x160 and keeping the voxel size the same. The images are currently >>> in analyze format but I have access to mri_convert and ImageConvert. >>> >>> Thank you. >>> >>> Sourav >> ___ >> 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 > > ___ > 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] Reduction of image size
Hi Sourav
that won't work - particularly if you are trying to crop in the a/s
dimension. Many brains might squeeze into 160 l/r but probably not all, and
certainly not with skull. And there won't be any consistent starting coord
as it will depend on where the head is in the FOV. The only way for it to
definitely work would be to downsample one dimension to 256/160=1.6mm. If
you skull strip you could get away with something higher res. Or use fewer
than 70 images.
cheers
Bruce
On Mon, 9 Feb 2015, SOURAV RANJAN KOLE wrote:
Hello Bruce,
Definitely, I am constructing atlases with these images. Based on the number
of available and functioning GPUs in our cluster, I am seemingly able to
construct atlases of ~70 images with each image size being 256x256x160 and
not of image size 256x256x256. Therefore, I am reslicing and I have not done
this before. Please guide me to determine the starting coordinates for
extraction. Thank you.
Regards,
Sourav
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Sunday, February 08, 2015 6:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Reduction of image size
Hi Sourav
Can you explain why you are reslicing?
Cheers
Bruce
On Feb 8, 2015, at 7:26 PM, SOURAV RANJAN KOLE wrote:
Thank you, again, Bruce.
How do I determine the starting coordinates for extraction, so I
do not cutoff relevant info?
Regards,
Sourav
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce
Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Sunday, February 08, 2015 5:04 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Reduction of image size
Hi Sourav
mri_extract
usage: mri_extract x0 y0 z0 dx dy dz
(x0, y0, z0) is the starting coordinate of the rectangle to
extract *not*
the size. (dx, dy, dz) is the size. Yours should be something
like:
mri_extract input.mgz 0 0 0 256 256 160 output.mgz
or maybe you don't want to start at 0, but further into the
volume.
Also, definitely do NOT use .img at any point as you will lose
direction
cosine info
cheers
Bruce
On Sun,
8 Feb 2015, SOURAV RANJAN KOLE wrote:
Hello Bruce,
Thank you for the prompt reply.
Although, mri_extract is creating new files but it
is giving me the following error- MRIextractInto:
bad src location (256, 256, 160). Also, ITK-SNAP
cannot read the new image file.
Here is what I am doing:
1. Converting from .mgz to .img
mri_convert brainmask.mgz brainmask.img --conform
--out_data_type float
2. Reducing size of image
mri_extract brainmask.img 256 256 160 1 1 1
new_brainmask.img
I would like the new images to be 256x256x160 and
voxel size to be 1x1x1. Am I not using mri_extract
correctly?
Thank you.
Regards,
Sourav
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf
of Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Sunday, February 08, 2015 4:12 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Reduction of image size
mri_extract should do the trick
Bruce
On Sun, 8 Feb 2015, SOURAV RANJAN KOLE
wrote:
Dear Freesurfer community,
Please let me know of an elegant way to
reduce image size from 256x256x256
to 256x256x160 and keeping the voxel
size the same. The images are currently
in analyze format but I have access to
mri_convert and ImageConvert.
Thank you.
Sourav
___
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 send
Re: [Freesurfer] Error in recon-all
Hi Noam it looks like the talairach alignment failed. You can usually find answers on our wiki for what to do in this type of case. For example: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_tktools cheers Bruce On Mon, 9 Feb 2015, Ben Eliezer, Noam wrote: Hi Freesurfer support, I am receiving an error from recon-all and would be happy to get your opinion. This dataset, I am processing, is generated by a 3D MPR (Sagittal orientation) protocol. It’s only one of many datasets I have and this is the only one giving me problems… The run seems to generate the typical directory listing: total 0 drwxrwxr-x 12 noambe staff 408 Feb 8 19:24 . drwxr-xr-x@ 20 noambe staff 680 Feb 9 07:49 .. drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 bem drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 label drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 mri drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 scripts drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 src drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 stats drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 surf drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 tmp drwxrwxr-x 4 noambe staff 136 Feb 8 19:27 touch drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 trash but the ‘mri’ folder, for example, is missing most of the data noambe-mac:03_FSseg noambe$ cd mri noambe-mac:mri noambe$ l total 50112 drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 . drwxrwxr-x 12 noambe staff 408 Feb 8 19:24 .. -rw-rw-r-- 1 noambe staff 21230 Feb 8 19:28 mri_nu_correct.mni.log -rw-rw-r-- 1 noambe staff 21230 Feb 8 19:26 mri_nu_correct.mni.log.bak drwxrwxr-x 3 noambe staff 102 Feb 8 19:25 orig -rw-rw-r-- 1 noambe staff 6915766 Feb 8 19:25 orig.mgz -rw-rw-r-- 1 noambe staff 21230 Feb 8 19:28 orig_nu.log -rw-rw-r-- 1 noambe staff 6175023 Feb 8 19:28 orig_nu.mgz -rw-rw-r-- 1 noambe staff 12484984 Feb 8 19:25 rawavg.mgz drwxrwxr-x 8 noambe staff 272 Feb 8 19:28 transforms noambe-mac:mri noambe$ The whole thing runs for a few minutes before it exists with errors. I’m attaching the output of the recon-all run. Thanks in advance, — Noam -- Noam Ben-Eliezer, PhD Adjunct Assistant Professor of Radiology Center for Biomedical-Imaging New-York University Medical School noam.ben-elie...@nyumc.org ___ 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] freesurfer in patients with brain volume loss after old injury or infarcts
Hi Salil in the end of the look valid there's not much more you can do. It would be on a case-by-case basis depending on the details of the lesion/surgery cheers Bruce On Tue, 10 Feb 2015, Salil Soman wrote: > Hi, > Is there an official thought on using freesurfer on cases were there is > volume loss after old stroke, or surgery, or trauma? I have a number of > cases were the results in general look reasonable for the remaining brain > tissue, and was was wondering if it is valid to use that data for analyses? > > Best wishes, > > Salil > > ___ 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] Map volume label to surface label
Hi Razib yes, I think mri_label2label will do this if you have reconstructed the surfaces. cheers Bruce On Tue, 10 Feb 2015, Muhammad Razib wrote: Hi, I am wondering is there a way in freesurfer to map manually labeled IBSR MRI .img/.hdr volume files to freesurfer surface file (e.g. lh.pial/rh.pial etc.) keeping the original labels? Thanks, Razib ___ 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] Parcellation
Hi Andre sorry, there is no way to run only part of the steps as there is lots of interdependancy. You need to run -all. That said, the new version that should be coming out in a couple of months is significantly faster and has a lot more openmp support. cheers Bruce On Wed, 11 Feb 2015, André Schmidt wrote: Dear free surfer experts, I intend to do a parcellation on my mprage images. The purpose of that is to use them further as seeds for tractography analysis. So far I used recon-all as follows: recon-all -subject xy -i xy.nii.gz -all But this is quite time-consuming and I want to ask for the command line for the parcellation only? Thanks a lot for your help Andre ___ 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] time critical problem: mri_ca_register failure during recon-all run
Hi Don are you running a single job on the 8G machine? What FS version? We haven't seen any core dumps in mri_ca_register recently. If you run it without openmp does it work? Kind of worrisome that it dies in a different place on a different machine Bruce On Wed, 11 Feb 2015, Krieger, Donald N. wrote: Dear list: We are under a significant deadline on which this freesurfer run depends. I’m reposting from last night along with a bit of additional information. A 2nd run on a different box yielded: nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) Also, the box on which the run detailed below was done has 8 GBytes of RAM, not 8 Mbytes – sorry about that. Any help and direction you can provide with this error would be appreciated. The full log is attached. I was running with –openmp 5 on a machine with 6 cores and 8 Mbytes of RAM. 0033: dt=73.984000, rms=0.641 (0.133%), neg=0, invalid=96777 0034: dt=73.984000, rms=0.640 (0.104%), neg=0, invalid=96777 0035: dt=73.984000, rms=0.640 (0.095%), neg=0, invalid=96777 0036: dt=517.888000, rms=0.639 (0.162%), neg=0, invalid=96777 0037: dt=23.12, rms=0.639 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... : dt=0.000, rms=0.639, neg=0, invalid=96777 0038: dt=92.48, rms=0.638 (0.081%), neg=0, invalid=96777 Segmentation fault (core dumped) ERROR: mri_ca_register with non-zero status 139 but continuing despite the error #-- #@# CA Reg Inv Tue Feb 10 19:24:19 EST 2015 /home/kriegerd/Contrib/freesurfer/subjects/175/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux OfficeFedora21 3.17.4-301.fc21.x86_64 #1 SMP Thu Nov 27 19:09:10 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 175 exited with ERRORS at Tue Feb 10 19:24:19 EST 2015 Regards, Don Signature0001 Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh ___ 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] time critical problem: mri_ca_register failure during recon-all run
Hi Don does it repeatably die in the same place when you run it with openmp 5? Are you sure nothing else was running at the time? Try running it with openmp 1 and make sure nothing else is running and see if it finishes sorry, not sure what else to suggest. If it dies in the same spot, upload the entire subject dir and let us know good luck Bruce On Wed, 11 Feb 2015, Krieger, Donald N. wrote: Thanks for responding so quickly, Bruce. Yes I was running a single job on the 6-core machine and have used it and this version of recon-all successfully before. The freesurfer instance was downloaded a few weeks ago - it is the Centos6 one. I don't know how to tell which version of the entire package it is. recon-all -version returns: $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ mri_ca_register -version returns: stable5 nu_estimate_np_and_em -version returns: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 preceded by a bunch of deprecation notices. ??? Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, February 11, 2015 9:39 AM To: Freesurfer support list Subject: Re: [Freesurfer] time critical problem: mri_ca_register failure during recon-all run Hi Don are you running a single job on the 8G machine? What FS version? We haven't seen any core dumps in mri_ca_register recently. If you run it without openmp does it work? Kind of worrisome that it dies in a different place on a different machine Bruce On Wed, 11 Feb 2015, Krieger, Donald N. wrote: Dear list: We are under a significant deadline on which this freesurfer run depends. I’m reposting from last night along with a bit of additional information. A 2nd run on a different box yielded: nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) Also, the box on which the run detailed below was done has 8 GBytes of RAM, not 8 Mbytes – sorry about that. Any help and direction you can provide with this error would be appreciated. The full log is attached. I was running with –openmp 5 on a machine with 6 cores and 8 Mbytes of RAM. 0033: dt=73.984000, rms=0.641 (0.133%), neg=0, invalid=96777 0034: dt=73.984000, rms=0.640 (0.104%), neg=0, invalid=96777 0035: dt=73.984000, rms=0.640 (0.095%), neg=0, invalid=96777 0036: dt=517.888000, rms=0.639 (0.162%), neg=0, invalid=96777 0037: dt=23.12, rms=0.639 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... : dt=0.000, rms=0.639, neg=0, invalid=96777 0038: dt=92.48, rms=0.638 (0.081%), neg=0, invalid=96777 Segmentation fault (core dumped) ERROR: mri_ca_register with non-zero status 139 but continuing despite the error #-- #@# CA Reg Inv Tue Feb 10 19:24:19 EST 2015 /home/kriegerd/Contrib/freesurfer/subjects/175/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux OfficeFedora21 3.17.4-301.fc21.x86_64 #1 SMP Thu Nov 27 19:09:10 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 175 exited with ERRORS at Tue Feb 10 19:24:19 EST 2015 Regards, Don Signature0001 Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh ___ 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] Interhemispheric registration of .mgh files
Hi Konrad you should be able to do this with mri_surf2surf, although the syntax might be tricky. cheers Bruce On Mon, 9 Feb 2015, Konrad Wagstyl wrote: > Hi all, > > We're having some trouble using interhemispheric registration. It works fine > for files that are automatically registered eg thickness, volume etc. but not > for mgh files, like ?h.w-g.pct.mgh. > Is there a way of adding files to xhemi/surf/ so that other surfaces files > can be compared between hemispheres? > > Thanks, > Konrad > ___ > 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] Freesurfer recon all error
Hi Bhavani those files don't list the error. Please see: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?highlight=%28reporting%29%7C%28error%29 for the information we need in order to be able to help you. cheers Bruce On Thu, 12 Feb 2015, Selvaraj, Bhavani wrote: > Hi > I tried running recon all command for two case study and it ended with error. > I am attaching the document. > Please could you help me solve this issue? > Thanks, > Bhavani > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of > freesurfer-requ...@nmr.mgh.harvard.edu > [freesurfer-requ...@nmr.mgh.harvard.edu] > Sent: Thursday, February 12, 2015 12:00 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Freesurfer Digest, Vol 132, Issue 15 > > Send Freesurfer mailing list submissions to >freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= > or, via email, send a message with subject or body 'help' to >freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at >freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. updating from 5.0 to 5.3 (Aaron Goldman) > 2. Re: Interhemispheric registration of .mgh files (Bruce Fischl) > 3. Help: error on running dt_recon (Sampada Sinha) > 4. Re: Help: error on running dt_recon (Douglas Greve) > 5. Re: Interhemispheric registration of .mgh files (Douglas Greve) > 6. Re: Interhemispheric registration of .mgh files (Douglas Greve) > 7. Re: Different results for GLM analysis of parcellated regions > and vertex-wise analyses (Bronwyn Overs) > 8. Re: updating from 5.0 to 5.3 (Harms, Michael) > 9. Re: DTI question (Thomas Potrusil) > 10. Re: bbregister error [Was: TRACULA mask error] (Worker, Amanda) > 11. Re: Interhemispheric registration of .mgh files (Konrad Wagstyl) > > > -- > > Message: 1 > Date: Wed, 11 Feb 2015 20:22:07 + > From: Aaron Goldman > Subject: [Freesurfer] updating from 5.0 to 5.3 > To: "freesurfer@nmr.mgh.harvard.edu" > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > I have a large set of images previously run in FreeSurfer 5.0. I'm also > preparing to run a new batch of images and debating whether to use 5.3 or > stick with 5.0. If I updated all the old datasets to 5.3, would I need to > visually QC them a second time, or are the versions similar enough that I can > rely on my pre-existing QC? Also, am I correct in assuming I shouldn't mix > versions 5.0 and 5.3? > > Thanks, > > Aaron > -- next part -- > An HTML attachment was scrubbed... > URL: > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20150211_0db58b38_attachment.html&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=5UcMVLhP4c-5tlXlhqydtYme5fk9N_47Aap066BmpS0&e= > > -- > > Message: 2 > Date: Wed, 11 Feb 2015 16:12:52 -0500 (EST) > From: Bruce Fischl > Subject: Re: [Freesurfer] Interhemispheric registration of .mgh files > To: Freesurfer support list > Cc: "sophie.adler...@ucl.ac.uk" > Message-ID: > > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Konrad > > you should be able to do this with mri_surf2surf, although the syntax > might be tricky. > > cheers > Bruce > On Mon, 9 Feb 2015, Konrad Wagstyl wrote: > >> Hi all, >> >> We're having some trouble using interhemispheric registration. It works fine >> for files that are automatically registered eg thickness, volume etc. but >> not for mgh files, like ?h.w-g.pct.mgh. >> Is there a way of adding files to xhemi/surf/ so that other surfaces files >> can be compared between hemispheres? >> >> Thanks, >> Konrad >> __
Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences?
Hi Silas you should certainly try to avoid a group-by-processing parameters bias. Is there a reason that one group would require different parameters than another? cheers Bruce On Mon, 16 Feb 2015, Silas wrote: > Hi Freesurfer team, > I'm currently making an structural analysis using freesurfer. In the > analysis i'm comparing 3 groups; 2 patient groups with different reactions > to a certain type of medication and a healthy control group. In the > freesurfer pipeline i'm changing the parameters wsthresh and wsgatlas in > order to obtain a better fitted pial surface and white matter surface - and > i was wondering if changing these parameters affect the comparability of the > 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? > > Best, Silas > > ___ 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] Entorhinal Cortex segmentation and volume
Hi Melina 1. Can you send us a picture? I'm not sure given your description, although the surfaces can be arbitrary in the hippocampus/amygdala and should be ignored there. 2. You should be able to use mri_label2vol for this. Note that you can load the label itself directly into freeview if you want without needing to run label2vol (but it will follow the white surface I believe and not fill the ribbon) cheers Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: > Hi experts, > I'm rather unexperienced with freesurfer so please excuse my basic > requests. > 1. I controlled the segmentation of the entorhinal cortex (EC) in over > 50 subjects following the borders described in Fischl 2009 (Predicting > the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg > aparc-aseg.mgz. > I noticed (esp. in the coronar slices and in approximately every mri) > brain tissue between amygdala/ hippocampus/ temporalpole and the EC > labelled as "none" or "ctx-?h-unknown". Has anything gone wrong with the > segmentation? Or is a label (e.g. perirhinal cortex) not loaded? > > 2. Is there a possibility to visualize the EC volume in freeview or > tkmedit from the exvivo.stats or exvivo.label file? I would like to > compare it to the other EC volume because they have very different > volumes. In the mail archive were similar questions about that but you > haven't answered them yet. > > Many thanks in advance, > Melina > ___ > 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] Changing wstresh and removing wsg-atlas - consequences?
I think that's ok. In the end you want the best models, you just need to make sure that there is no significant group-by-parameters interaction. Not intervening can also cause a bias. For example if there is atrophy in one group that allows the surfaces to avoid dura but in the other group significant dura is included you will overestimate effect sizes cheers Bruce On Mon, 16 Feb 2015, Silas wrote: Hi Bruce, Thanks for your answer. My data quality isn't always as good as i could have hoped. This unfortunately impairs freesurfers ability to distinguish between grey matter surface, dura and skull. In specific cases I've found it rewarding to change the parameters in order to gain a better fitting of the pial surface to the actual grey matter surface. Afterwards I've made manual editing to obtain the best possible fit. These parameter changes isn't group specific. Would you still avoid changing the parameters? Best, Silas > Date: Mon, 16 Feb 2015 09:28:05 -0500 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences? > > Hi Silas > > you should certainly try to avoid a group-by-processing parameters bias. > Is there a reason that one group would require different parameters than > another? > > cheers > Bruce > On Mon, 16 Feb 2015, Silas wrote: > > > Hi Freesurfer team, > > I'm currently making an structural analysis using freesurfer. In the > > analysis i'm comparing 3 groups; 2 patient groups with different reactions > > to a certain type of medication and a healthy control group. In the > > freesurfer pipeline i'm changing the parameters wsthresh and wsgatlas in > > order to obtain a better fitted pial surface and white matter surface - and > > i was wondering if changing these parameters affect the comparability of the > > 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? > > > > Best, Silas > > > > > ___ > 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] Freesurfer with whole brain T1 and partial coverage FLAIR
Hi Ajay if it covers the whoe brain you might be ok, try it and see how it goes Bruce On Wed, 18 Feb 2015, Ajay Kurani wrote: Hello Freesurfer experts, I have a question regarding the use of the -T2 and -FLAIR flags in freesurfer. I have 2 scans: 1 whole brain MPRAGE and 1 partial brain FLAIR (bottom of cerebellum/brainstem gets cut off on some subjects). I wanted to see if freesurfer would still be able to run correctly if my FLAIR image is aligned, BUT DOES NOT COVER the exact same amount of the brain as my MPRAGE? I checked with autorecon1 and the mask seemed to cover the whole brain, however I am not sure if there are any subsequent steps that might not behave properly such lesion detection, surface creation etc. Thanks, Ajay ___ 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] Thin Surface
can you check mri_segmet and mris_make_surfaces and see if the auto-detected intensity parameters are reasonable? Things like max gray at csf border and such. If not, you can set them explicitly using the expert opts - this usually works Bruce On Wed, 18 Feb 2015, Pedro Rosa - Gmail wrote: Hi, I am resending it once I could not find it in the archives. Thanks, Pedro. Dear Freesurfers, I am working on a 1.5T MPRAGE sample of first-episode psychosis and controls, and have found that some subjects end up having thin cortical surfaces with frequent unsegmented deep sulci. I think this was worse with FreeSurfer 5.3 than with FreeSurfer 5.1. I attached some screen shots of aparc+aseg labeling T1.mgz from a few of these subjects. This seems to be a widespread cortical issue, although it was heterogeneous across subjects (some of them seemed to have the “caudal half" of both hemispheres adequately segmented), and trying to simply rerun those subjects was not very helpful. Should I manually work on them, rerun recon-all with distinct parameters, or just discard them? Regards, Pedro Rosa. ___ 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] Thin Surface
Hi Pedro I can't tell - you need to click around in the images and see what you think Bruce On Wed, 18 Feb 2015, Pedro Rosa - Gmail wrote: Thanks, Bruce. I pasted the mri_segment and mris_make_surfaces I found in three subjects’ logs. Expert opts would be -seg-wlo and -seg-ghi? Which values would be reasonable? Do they depend on scanning characteristics or do you have a sort of standard parameters for the software? Regards, Pedro Rosa. Subject 1: #@# WM Segmentation Mon Feb 16 09:08:56 BRST 2015 \n mri_segment brain.mgz wm.seg.mgz \n doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 105.0 +- 4.5 [80.0 --> 125.0] GM (72.0) : 70.1 +- 13.5 [30.0 --> 96.0] setting bottom of white matter range to 83.6 setting top of gray matter range to 97.1 Subject 2: WM (105.0): 105.6 +- 4.6 [80.0 --> 125.0] GM (70.0) : 68.4 +- 13.5 [30.0 --> 96.0] setting bottom of white matter range to 81.9 setting top of gray matter range to 95.4 Subject 3: WM (105.0): 105.6 +- 4.3 [80.0 --> 125.0] GM (71.0) : 69.2 +- 13.9 [30.0 --> 96.0] setting bottom of white matter range to 83.2 setting top of gray matter range to 97.1 —— Subject 1: \n mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs Subject2 lh \n only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/filled.mgz... reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/brain.finalsurfs.mgz... reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/wm.mgz... 14199 bright wm thresholded. 1723 bright non-wm voxels segmented. reading original surface position from /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/surf/lh.orig... computing class statistics... border white: 347738 voxels (2.07%) border gray 336007 voxels (2.00%) WM (95.0): 96.2 +- 6.5 [70.0 --> 110.0] GM (85.0) : 81.4 +- 13.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.8 (was 70) setting MAX_BORDER_WHITE to 105.5 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 44.5 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.3 (was 40) Subject 2: setting MIN_GRAY_AT_WHITE_BORDER to 70.2 (was 70) setting MAX_BORDER_WHITE to 106.6 (was 105) setting MIN_BORDER_WHITE to 84.0 (was 85) setting MAX_CSF to 56.4 (was 40) setting MAX_GRAY to 93.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.5 (was 40) Subject 3: WM (97.0): 97.9 +- 6.2 [70.0 --> 110.0] GM (87.0) : 83.8 +- 13.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) setting MAX_BORDER_WHITE to 107.2 (was 105) setting MIN_BORDER_WHITE to 85.0 (was 85) setting MAX_CSF to 57.9 (was 40) setting MAX_GRAY to 94.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 78.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.4 (was 40) On Wednesday, February 18, 2015 at 7:58 PM, Bruce Fischl wrote: can you check mri_segmet and mris_make_surfaces and see if the auto-detected intensity parameters are reasonable? Things like max gray at csf border and such. If not, you can set them explicitly using the expert opts - this usually works Bruce On Wed, 18 Feb 2015, Pedro Rosa - Gmail wrote: Hi, I am resending it once I could not find it in the archives. Thanks, Pedro. Dear Freesurfers, I am working on a 1.5T MPRAGE sample of first-episode psychosis and controls, and have found that some subjects end up having thin cortical surfaces with frequent unsegmented deep sulci. I think this was worse with FreeSurfer 5.3 than with FreeSurfer 5.1. I attached some screen shots of aparc+aseg labeling T1.mgz from a few of these subjects. This seems to be a widespread cortical issue, although it was heterogeneous across subjects (some of them seemed to have the “caudal half" of both hemispheres adequately segmented), and trying to simply rerun those subjects was not very helpful. Should I manually work on them, rerun recon-all with distinct parameters, or just discard them? Regards, Pedro Rosa. ___ 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
Re: [Freesurfer] visualize subcortical areas in tksurfer?
Hi Daniel no, tksurfer visualizes surfaces exclusively, and the subcortical structures are volumetric by and large. You could tesselate their surface and view it in tksurfer, or just use tkmediit or freeview. cheers Bruce On Thu, 19 Feb 2015, Yang, Daniel wrote: > Dear FreeSurfer experts, > > I find that tksurfer allows me to visualize subcortical areas such as > hippocampus. The > visualization looks valid to me. > > Can tksurfer be used in this way? > > Thanks!! > Daniel > > ___ 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] visualize subcortical areas in tksurfer?
HI Daniel no, that won't work. Vol2surf samples a volume to an existig surface and none of the subcortical structures will be anywere near the cortical surface. You would need to run mri_tessellate on each subcortical label that you want to generate a surface for, but I'm still not sure what you are trying to do. cheers Bruce On Fri, 20 Feb 2015, Yang, Daniel wrote: > Hi Bruce, > > Thanks! and yes, I used mri_vol2surf to convert subcortical region as a > volume file to surface (mgh file) and then visualize it with tksurfer. > According to what you said, this is still valid, right? > > Best, > Daniel > > On 2/19/15, 5:59 PM, "Bruce Fischl" wrote: > >> Hi Daniel >> >> no, tksurfer visualizes surfaces exclusively, and the subcortical >> structures are volumetric by and large. You could tesselate their surface >> and view it in tksurfer, or just use tkmediit or freeview. >> >> cheers >> Bruce >> On Thu, 19 Feb >> 2015, Yang, Daniel wrote: >> >>> Dear FreeSurfer experts, >>> >>> I find that tksurfer allows me to visualize subcortical areas such as >>> hippocampus. The >>> visualization looks valid to me. >>> >>> Can tksurfer be used in this way? >>> >>> Thanks!! >>> Daniel >>> >>> >> ___ >> 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 >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >> ianceline&d=AwIBAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MORXy6GkKdTAw3V58rxz >> UZGOKpGXPDgqUHY&m=GwXYm_UFsMTK666w58RNVUgITnGz6y7wSvA4OWe3VDI&s=X6YOsg4F5k >> hF6_1eRhIIXjcpNfRIveb8xbtz9jVs7Rk&e= . 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.
Re: [Freesurfer] manually drawn ROI mean thickness extraction
Hi Claudia I think mris_anatomical_stats can take a label file, which would do the trick cheers Bruce On Fri, 20 Feb 2015, Claudia Dacquino wrote: Dear all freesurfers, I have manually drawn a region of interest and saved it as a label file in the /label folder and I now want to extract mean thickness of this ROI. How can I do it?Thanks a lot Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 51501575 web: http://www.neuropsichiatrialab.com ___ 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] A different question, pial problems near a temporal lesion
Hi Mark no, that can be tough as it breaks many of our laminar assumptions. sorry Bruce On Tue, 17 Feb 2015, Mark Fletcher wrote: Dear FreeSurfer Development Team, An additional, but different question. One of my subjects has some sort of hole (lesion) in the left temporal lobe (slides 3-5). I have attached a powerpoint with screenshots in order to visualize the issue ( http://gate.nmr.mgh.harvard.edu/filedrop2/?p=3pr4d21hyxi ) I have attempted (unsuccessfully) many times to get FreeSurfer to trace the pial matter superior to this lesion. I tried adding control points to many regions around it. I have also tried edits to the white matter, treating it as a white matter geometric inaccuracy (or hole) by following the instructions here(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freev iew ). Do you have any other suggestions that might help? By the way, I am using the latest version of FreeSurfer (5.3.0) with a 3T Siemens TRIO. ___ 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] visualize subcortical areas in tksurfer?
Hi Daniel I wouldn't advise this - you will miss most of the activation unless it happens to be right next to where the surface runs adjacent to the structure of interest. For subcortical structures you are better off showing the results in slices. cheers Bruce On Mon, 23 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks for the reply. My main question is how to best visualize subcortical activation in a figure. Sometimes we do see some subcortical activation (like the attached, which is a random search) (if the attachment does not work, please see the examplehere: http://www.frontiersin.org/files/Articles/18483/fnhum-06-00021-HTML/ image_m/fnhum-06-00021-g003.jpg). Is it okay to visualize such subcortical activation via tksurfer? If not, could you please recommend a method to visualize subcortical activation? Sincerely, Daniel On 2/20/15, 9:06 AM, "Bruce Fischl" wrote: HI Daniel no, that won't work. Vol2surf samples a volume to an existig surface and none of the subcortical structures will be anywere near the cortical surface. You would need to run mri_tessellate on each subcortical label that you want to generate a surface for, but I'm still not sure what you are trying to do. cheers Bruce On Fri, 20 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks! and yes, I used mri_vol2surf to convert subcortical region as a volume file to surface (mgh file) and then visualize it with tksurfer. According to what you said, this is still valid, right? Best, Daniel On 2/19/15, 5:59 PM, "Bruce Fischl" wrote: Hi Daniel no, tksurfer visualizes surfaces exclusively, and the subcortical structures are volumetric by and large. You could tesselate their surface and view it in tksurfer, or just use tkmediit or freeview. cheers Bruce On Thu, 19 Feb 2015, Yang, Daniel wrote: Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl ianceline&d=AwIBAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHY&m=GwXYm_UFsMTK666w58RNVUgITnGz6y7wSvA4OWe3VDI&s=X6YOsg4F5k hF6_1eRhIIXjcpNfRIveb8xbtz9jVs7Rk&e= . 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli anceline&d=AwIBAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MORXy6GkKdTAw3V58rxzUZ GOKpGXPDgqUHY&m=cue78znVQSK09ZAzgx1bpMEP_Q1FH_tPiP6u951nI6I&s=FTUF8bxfkijut U0D90a6nXk4E6QXECVzI7RktBWSD04&e= . 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] RAM Replace
I would very much hope that replacing the RAM wouldn't change anything Bruce On Mon, 23 Feb 2015, Pedro Rosa - Gmail wrote: > Dear all, > I would like to know whether a RAM memory replacement in a Mac computer would > change > FreeSurfer 5.3 processing. > I have a sample that was almost completely processed, but there are a few > subjects > whose acquisition are yet to be done. I would like know whether I could > process such > images after the RAM replacement without biasing the study. The change would > be from > a Markvision without ECC (error-correction code) to a Kingston with ECC. > Thanks in advance, > Pedro Rosa. > > > ___ 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] RAM Replace
yes, it would be pretty strange if swapping out ram changed the results On Mon, 23 Feb 2015, Pedro Rosa wrote: > Thanks, Bruce. > I am asking this because I believe that changing the processor or the > operational system could change the processing. If I got it correctly, it is > expected that it is not the same for the RAM. Am I correct? > Thanks again, > Pedro. > >> On Feb 23, 2015, at 21:50, Bruce Fischl wrote: >> >> I would very much hope that replacing the RAM wouldn't change anything >> Bruce >> On >> Mon, 23 Feb 2015, Pedro Rosa - Gmail wrote: >> >>> Dear all, >>> I would like to know whether a RAM memory replacement in a Mac computer >>> would change >>> FreeSurfer 5.3 processing. >>> I have a sample that was almost completely processed, but there are a few >>> subjects >>> whose acquisition are yet to be done. I would like know whether I could >>> process such >>> images after the RAM replacement without biasing the study. The change >>> would be from >>> a Markvision without ECC (error-correction code) to a Kingston with ECC. >>> Thanks in advance, >>> Pedro Rosa. >> ___ >> 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
Re: [Freesurfer] Desikan-Kilany atlas
Hi Norman perhaps you can take a step back and tell us what you want to use it for? We might be able to suggest a better analysis strategy Bruce On Tue, 24 Feb 2015, Norman Benbrahim wrote: > Hi, > I want to use the Desikan-Kilany atlas to run some analysis in some regions, > however > I am very new to freesurfer. What I would like to accomplish is the following: > 1) Transform the atlas into MNI152 2mm space > 2) Convert the atlas to a binary nifti image (similarly to the way FSL's > atlases are > stored) > If anyone can help me get started that would be awesome. Thank you! > -Norman > > ___ 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] Desikan-Kilany atlas
I see. You could do what you want by sampling the ?h.aparc.annot into the volume (mri_surf2vol), then mapping into MNI space (mri_vol2vol). Actually, if you do surf2vol from fsaverage I think it's already in MNI coords, but Doug can confirm. The problem is going to be that the mapping won't be very accurate across subjects. You would be better off doing it all on the surface cheers Bruce On Tue, 24 Feb 2015, Norman Benbrahim wrote: No problem, I want to take certain regions and use them as masks in order to compute the joint histogram between a thresholded z-score map obtained from ICA (a resting state network) masked in that region, and the variance of the BOLD image. I already have scripts set up to do this in matlab, so I would only need the atlas in nifti format so I can pick out which regions to use (using the rich club paper, van den Heuvel et al. 2011), and create masks out of those. On Tue, Feb 24, 2015 at 4:22 PM, Bruce Fischl wrote: Hi Norman perhaps you can take a step back and tell us what you want to use it for? We might be able to suggest a better analysis strategy Bruce On Tue, 24 Feb 2015, Norman Benbrahim wrote: > Hi, > I want to use the Desikan-Kilany atlas to run some analysis in some regions, however > I am very new to freesurfer. What I would like to accomplish is the following: > 1) Transform the atlas into MNI152 2mm space > 2) Convert the atlas to a binary nifti image (similarly to the way FSL's atlases are > stored) > If anyone can help me get started that would be awesome. Thank you! > -Norman > > ___ 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] Desikan-Kilany atlas
Hi Norman don't give it the gcs file as input - that's the atlas. Give it the lh.aparc.annot for that subject cheers Bruce On Wed, 25 Feb 2015, Norman Benbrahim wrote: Thanks for your reply Bruce, however I get an error when try to use this command. I'm in the directory containing the files and I ran mri_surf2vol --surfval lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs --hemi lh --outvol LH.nii and it gave me an output of ERROR: cannot recognize the type of lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs On Tue, Feb 24, 2015 at 4:42 PM, Bruce Fischl wrote: I see. You could do what you want by sampling the ?h.aparc.annot into the volume (mri_surf2vol), then mapping into MNI space (mri_vol2vol). Actually, if you do surf2vol from fsaverage I think it's already in MNI coords, but Doug can confirm. The problem is going to be that the mapping won't be very accurate across subjects. You would be better off doing it all on the surface cheers Bruce On Tue, 24 Feb 2015, Norman Benbrahim wrote: No problem, I want to take certain regions and use them as masks in order to compute the joint histogram between a thresholded z-score map obtained from ICA (a resting state network) masked in that region, and the variance of the BOLD image. I already have scripts set up to do this in matlab, so I would only need the atlas in nifti format so I can pick out which regions to use (using the rich club paper, van den Heuvel et al. 2011), and create masks out of those. On Tue, Feb 24, 2015 at 4:22 PM, Bruce Fischl wrote: Hi Norman perhaps you can take a step back and tell us what you want to use it for? We might be able to suggest a better analysis strategy Bruce On Tue, 24 Feb 2015, Norman Benbrahim wrote: > Hi, > I want to use the Desikan-Kilany atlas to run some analysis in some regions, however > I am very new to freesurfer. What I would like to accomplish is the following: > 1) Transform the atlas into MNI152 2mm space > 2) Convert the atlas to a binary nifti image (similarly to the way FSL's atlases are > stored) > If anyone can help me get started that would be awesome. Thank you! > -Norman > > ___ 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] Analyze format
Hi Pablo the mat file is an extension to analyze the specifies the direction cosines. Without it we are only guessing at the anatomical orientation of the image. Unless these images have some marker such as a vitamin E capsule how will you ever know if we got left/right correct? cheers Bruce On Wed, 25 Feb 2015, pablo najt wrote: Dear FS experts,I am trying to run recon-all on data with analyze format. I am aware that this is not the best format, however I do not have DICOM or NIFTI original data as this is a very old data from University of North Carolina. When I run import the images with recon-all -i. I am getting the following log below. Do you advice to proceed with recon-all -all or do you there is a way I could obtain the mat file that freesurfer is asking? Thank you Pablo recon-all -i 30225.img -s 30225 mri_convert /home/0116442s/FS_test/30225.img /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz mri_convert /home/0116442s/FS_test/30225.img /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz - INFO: could not find /home/0116442s/FS_test/30225.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped. INFO: if not valid, please provide the information in /home/0116442s/FS_test/30225.mat file - $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/0116442s/FS_test/30225.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, 1) k_ras = (0, 1, 0) writing to /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz... #-- recon-all -s 30225 finished without error at Wed Feb 25 15:30:09 GMT 2015 done ___ 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] Any short route to parcellate only?
Hi Dorian, no, sorry, you pretty much need to run everything to get it. cheers Bruce On Wed, 25 Feb 2015, Dorian P. wrote: Hi folks, I am using the parcellation of Freesurfer for some other analyses. I see that the parcellation if obtained rather late in the pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all However, asking does not hurt: is there any short route to get the Desikan parcellation without doing the entire recon-all pipeline? I am not interested in thickness, template registration, etc. I need only the parcellation of gray matter in native space. Advice on other tools that can run parcellation quickly is also welcome. Dorian UPenn ___ 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] warping segmentations onto unprocessed brain
Is there any reason you need it to be nonlinear? I would think bbregister and mri_vol2vol would do the trick Cheers Bruce > On Feb 25, 2015, at 11:18 PM, David Grayson wrote: > > Hi freesurfers, > > I am hoping to warp an aparc+aseg.mgh file from a subject's > freesurfer-processed image to a separate (unprocessed) T1 image on the same > subject. I would like to use a purely intensity-based nonlinear volumetric > registration to do this, to save time and complication. I understand I can do > this if I have a .m3z warp file. > > My question is, how can I get this warp file? I have tried using > mri_cvs_register with the --step3 option, but that appears to only work after > the surface-based registrations have been carried out. I haven't found > another tool to do this yet. > > Are there any ideas? Thank you very much for your time. > > -David > ___ > 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] Analyze format
Hi Pablo I really don't know the analyze conventions or whether this will work. If you are sure of the orientation then convert it to mgz and check in tkmedit whether we got the orientation right (that is that the left side of the brain is properly identified as such in tkmedit/freeview) cheers Bruce On Thu, 26 Feb 2015, pablo najt wrote: Thank you Bruce for the piece of mind. The images were neurologically oriented (L=L) for analysis with SPM. Do you know if this helps at all? Thanks Pablo Date: Wed, 25 Feb 2015 10:44:48 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Analyze format Hi Pablo the mat file is an extension to analyze the specifies the direction cosines. Without it we are only guessing at the anatomical orientation of the image. Unless these images have some marker such as a vitamin E capsule how will you ever know if we got left/right correct? cheers Bruce On Wed, 25 Feb 2015, pablo najt wrote: > Dear FS experts,I am trying to run recon-all on data with analyze format. I > am aware that this is not the best format, however I do not have DICOM or > NIFTI original data as this is a very old data from University of North > Carolina. > > When I run import the images with recon-all -i. I am getting the following > log below. Do you advice to proceed with recon-all -all or do you there is a > way I could obtain the mat file that freesurfer is asking? > Thank you > Pablo > recon-all -i 30225.img -s 30225 > > > mri_convert /home/0116442s/FS_test/30225.img > /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz > > mri_convert /home/0116442s/FS_test/30225.img > /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz > - > INFO: could not find /home/0116442s/FS_test/30225.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped. > INFO: if not valid, please provide the information in > /home/0116442s/FS_test/30225.mat file > - > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /home/0116442s/FS_test/30225.img... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, 1) > k_ras = (0, 1, 0) > writing to /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz... > > #-- > > recon-all -s 30225 finished without error at Wed Feb 25 15:30:09 GMT > 2015 > done > > > > ___ 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 and subcortical regions
Hi Andre sorry, I don't remember how many regions there are. Should be easy enough to count in matlab. For the tractography question you'll have to wait for Anastasia to respond Bruce On Thu, 26 Feb 2015, André Schmidt wrote: Hi Bruce, Thanks, yes I see these files in the mri folder. I like to use the apart.a2009s+aseg.mgz file (how many regions are included in this file?) now for tractography (every region as a seed mask) using probtrackx (sorry). How can I create a text file with all these seed regions (including their path)? Thanks again Andre Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 26. Februar 2015 15:13 An: Freesurfer support list Betreff: Re: [Freesurfer] recon-all and subcortical regions Hi Andre if you ran recon-all you will have created a volume file names aseg.mgz that has the subcortical segmentation (and an aparc+aseg.mgz that has both subcortical and cortical in it) cheers Bruce On Thu, 26 Feb 2015, André Schmidt wrote: Dear experts, I use recon-all for the parcellation of my MPRAGE. As far as I can see this procedure does not address subcortical regions - right? How can I additionally perform a parcellation of subcortical regions? Many thanks for your help Andre ___ 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] recon-all and subcortical regions
Hi Andre if you ran recon-all you will have created a volume file names aseg.mgz that has the subcortical segmentation (and an aparc+aseg.mgz that has both subcortical and cortical in it) cheers Bruce On Thu, 26 Feb 2015, André Schmidt wrote: Dear experts, I use recon-all for the parcellation of my MPRAGE. As far as I can see this procedure does not address subcortical regions - right? How can I additionally perform a parcellation of subcortical regions? Many thanks for your help Andre ___ 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] warping segmentations onto unprocessed brain
Hi David yes, you can use bbregister to do the rigid alignment, then use it as initialization for mri_nl_align. I would think you are better off doing the surface recons and using cvs though. It's only computer time cheers Bruce On Wed, 25 Feb 2015, David Grayson wrote: > Hey Bruce, > Thanks for responding. I would actually prefer nonlinear. I did not mention > it, but the aseg data that I have is on a distortion-corrected T1 image, > whereas the unprocessed image I want to warp onto is the same scan but not > corrected for distortion. The distortions are nonlinear. I was hoping there > might be a way to get a warp field to go between the two images without > running both images through the recon-all pipeline. Are there any other > possible tools? > > Thanks! > -David > > On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl > wrote: > Is there any reason you need it to be nonlinear? I would think > bbregister and mri_vol2vol would do the trick > Cheers > Bruce > > > > > On Feb 25, 2015, at 11:18 PM, David Grayson >wrote: > > > > Hi freesurfers, > > > > I am hoping to warp an aparc+aseg.mgh file from a subject's > freesurfer-processed image to a separate (unprocessed) T1 image > on the same subject. I would like to use a purely > intensity-based nonlinear volumetric registration to do this, to > save time and complication. I understand I can do this if I have > a .m3z warp file. > > > > My question is, how can I get this warp file? I have tried > using mri_cvs_register with the --step3 option, but that appears > to only work after the surface-based registrations have been > carried out. I haven't found another tool to do this yet. > > > > Are there any ideas? Thank you very much for your time. > > > > -David > > ___ > > 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
Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Sarah
have you used mri_vol2surf to sample the data onto the surface? When you
say "extract specific regions of functional data from a flat " do you
want to average within the ROI?
cheers
Bruce
On Thu, 26 Feb 2015, Sarah Finnegan wrote:
I have a question about the equivalent of fslmaths -mas option in
freesurfer.
I have several manually defined labels in .label form that I want to use to
extract specific regions of functional data from a flat patch. Ordinarily in
fsl I would just use
fslmaths -invol {functional_data} -mas {bin_label} -outvol
{masked_functional_data}
but I'm a little confused about an equivalent for this in free surfer as I
don't want to perform any further stats on these ROI yet, extract them from
any surrounding data and overlay onto the flattened surface.
I have tried using
mri_vol2roi --label {V2_rh.label} --srcvol {functional_data.mgz} --srcreg
{anat2exf.register.dat} --roiavg {func_V2_mask} --finalmskvol
{func_V2_mask_out}
but when overlaying the output file there are no data points visible.
Any help would be great as several other functions that I have tried seem to
be obsolete,
Thanks!
Sarah
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Re: [Freesurfer] Extract values in ROI to ascii file
Hi Ruthger sorry, I don't think we have anything to do exactly what you want. It would be easy enough to do in matlab though cheers Bruce On Fri, 27 Feb 2015, Righart, Ruthger wrote: > Dear Freesurfers, > > I am using mris_convert to obtain per vertex thickness values in an > ascii file. > > What I would like to do is to limit the requested area to a certain > region of interest using a label file. Is this possible? (analogous to > mris_anatomical_stats where a label flag can be given?). > > Thank you very much in advance & all the best! > > Ruthger > ___ > 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] reconstructing from T2 scan
it if's a T1-weighted flash that should work cheers Bruce On Mon, 2 Mar 2015, Satrajit Ghosh wrote: hi bruce, we are missing a T1 scan from a participant. is there any pathway in freesurfer to reconstruct from the T2-flair/flash scan? cheers, satra ___ 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 overlay threshold
you can use the command: set_current_threshold_from_percentile(min, mid,max) which will compute the thresholds based on the histogram of values On Tue, 3 Mar 2015, Douglas N Greve wrote: > > I'm not sure what you mean. optimal in what sense? > doug > > On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote: >> Hi Fs experts, >> >> I had a quick question about settings thresholds of surface overlays >> in Tksurfer. I am currently generating images of the thickness, volume >> and surface area of individual subjects, and would like to know if >> there are optimal minimum and maximum threshold values to be set for >> different surfaces. For example, when overlaying thickness (from >> /surf/?h.thickness), I have set the min threshold to 1 or 1.3 (see >> attached); however I'm not sure this same threshold holds up in the >> other surfaces (e.g. surface area). >> >> In summary, is there an optimal way to determine what this min. and >> max. threshold should be in function of the distribution displayed in >> the threshold window (see attached, on the left)? >> >> Thank you! >> >> Gabriella >> >> >> ___ >> 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] Fwd: Recon-all Error
Hi Hassan you need to add some directives to recon-all to tell it what to do. For example, if you add "-all" to your command line it will do everything it knows how to (pretty much) cheers Bruce On Wed, 4 Mar 2015, Hassan bakhshi wrote: HI, Im using freesurfer newly, i have a folder of a subject's MRI's named 139942 I tried to run recon-all of a File named I000 The point is to get Superior temporal gyrus thickness. but it show an error and stop working. i looked up archive of FAQ's but i didnt anything usefull. There is the recon-all log attached! Please Help! By the way I'm using Ubuntu 14.04 LTS!! ___ 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] label
Hi Fabrizio the strange error message is a bug in our reporting (which I just fixed), but it isn't the source of your problem. Does the cortex.label file exist? Note that you are specifying the right hemi label file for the left hemi stats, which is almost certainly wrong. I also don't think you need to specify the path to the label file, it assumes it is in subjid/label (so just -l lh.cortex.label should be sufficient) cheers Bruce On Wed, 4 Mar 2015, Fabrizio Piras wrote: > Dear FreeSurfers, > I need to extract mean thickness from a manually defined label which is now > in subjid/label (named mpfc.label) > I tried with mris_anatomical_stats using the -l flag but here is what I got > > iMac-di-Mac:label fabriziopiras$ mris_anatomical_stats -l > subjid/label/rh.cortex.label -b subjid lh limiting computations to label > subjid/label/rh.cortex.label. reading volume > /Volumes/immagini/freesurfer/subjects/subjid/mri/wm.mgz... reading input > surface /Volumes/immagini/freesurfer/subjects/subjid/surf/lh.white... > reading input pial surface > /Volumes/immagini/freesurfer/subjects/subjid/surf/lh.pial... reading > input white surface > /Volumes/immagini/freesurfer/subjects/subjid/surf/lh.white... No such > file or directory mris_anatomical_stats: could not open label file > subjid/label/rh.cortex.label No such file or directory subjid: could not > read label file ` > The problem does not seem to depend on the label I created since I also tried > with rh.cortex.label which was done by freesurfer itself with same results > Does anybody know why? > Thank you in advance > > -- > Fabrizio Piras PhD > -- > Laboratorio di Neuropsichiatria > Dipartimento di Neurologia Clinica e Comportamentale > IRCCS Fondazione Santa Lucia > via Ardeatina 306 - 00179 Roma > Tel. +39 (0)6 51501363 > Fax +39 (0)6 51501213 > web: http://www.neuropsichiatrialab.com > > > ___ > 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] tksurfer overlay threshold
Hi Gabriela they set the threshold so that 92% of the values are not displayed, and the color scale saturates at the 99 percentile cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > Thanks Bruce! > > I tried using the command: > > sclv_set_current_threshold_from_percentile > > The tried using the values .92, .925, .99 as noted on the wiki but I'm still > not quite sure what these percentages do in terms of setting the threshold? > > Thanks! > Gabriella > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Tuesday, March 03, 2015 7:05 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] tksurfer overlay threshold > > you can use the command: > > set_current_threshold_from_percentile(min, mid,max) > > which will compute the thresholds based on the histogram of values > > On Tue, 3 Mar 2015, Douglas N Greve wrote: > >> >> I'm not sure what you mean. optimal in what sense? >> doug >> >> On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote: >>> Hi Fs experts, >>> >>> I had a quick question about settings thresholds of surface overlays >>> in Tksurfer. I am currently generating images of the thickness, >>> volume and surface area of individual subjects, and would like to >>> know if there are optimal minimum and maximum threshold values to be >>> set for different surfaces. For example, when overlaying thickness >>> (from /surf/?h.thickness), I have set the min threshold to 1 or 1.3 >>> (see attached); however I'm not sure this same threshold holds up in >>> the other surfaces (e.g. surface area). >>> >>> In summary, is there an optimal way to determine what this min. and >>> max. threshold should be in function of the distribution displayed in >>> the threshold window (see attached, on the left)? >>> >>> Thank you! >>> >>> Gabriella >>> >>> >>> ___ >>> 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
