[Freesurfer] Qdec Outputs - Looking For Statistical Maps To Overlay In SurfStat
Dear Freesurfer List I am trying to use SurfStat to create figures based on my qdec results. However, I cannot figure out what outputs form qdec are what, or what their iunits are. I cannot find a description of qdec's outputs on the Freesurfer Wiki. 1) I want to find the statistic overlay for my contrast of interest. Qdec creates a folder for each possible test I could make based on the design. For exasmple, I would like to overlay the results from the folder lh-Avg-thickness-TESSF-Cor. I think I want to use the gamma.mgh file as my overlay. Is that the true? I have some questions about the units of the gamma.mgh files though. When I use SurfStat, it automatically scales this at -0.2 - 0.2. I assumed this was the Anti- Long P scale used by qdec, so I tried to rescale my display to match the colorscale I use to display results in qdec. However, when I tried to change the scale to -3 - > 3, I get nothing. In qdec, I do see effects using this exact scale( min 1.3, max 3, min -1.3, max -3). So This suggests to me that the gamma.mgh is not in the same units (not anti-log(-p)). What are the units? 2) I was told that qdec saves a mean thickness file. I was also told it was one of the gamma.mgh files. Qdec creates a folder for each hemisphere called, for example, lh-Avg-Intercept-thickness. I assumed this was the correct overlay, but it looked to be demeaned as it had both negative a positive values. Is it demeaned? Is there a file that qdec saves that is just thickness? Or is there a way to manipulate the files so that they are not demeaned? Thank you for your assistance Best regards, Jennifer Bramen, Ph.D. Assistant Research Neuroscientist David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbra...@mednet.ucla.edu Campus Mail Code 176919 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cannot Configure Segmentation Brush WHen Editing Subcortical Parcellations
Dear Freesurfer Support Cut-and-paste the following info into your FreeSurfer problem report: - FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Kernel info: Darwin 9.8.0 i386 - Please include the following additional information in your report: 1) subject name 6002 2) the entire command-line executed tkmedit 6002 brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white - segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt & 3) the error message generated n/a I am trying to edit the subcortical parcellations. I found the wiki instructions, and have followed (I think) to a t. I am unable to effect the Segmentation Brush label by using the Configure Segmentation Brush menu. But regardless of my selection, my drawing is labeled "out of bounds". I have updated to the most recent version of Freesurfer. I also attempted to use an older version, in case it was a recent bug, incompatible with recon-all done in an older version, etc. However, no version changes have helped. Can someone tell me what I am missing? FYI - When I select a label type, I have tried both having the "Segmenmtation Brush Info" window open, with my slection highlighted, and highlighting and closing the window. I am hoping I am simply missing a step though obvious to the wiki creator. Here is the link to the "Editing" instructions I have been following: http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations 4) optionally include the subject's /script/recon-all.log (n/a) Thanks for your assistance. Best regards, Jennifer Bramen, Ph.D. Assistant Research Neuroscientist UCLA Center for Cognitive Neuroscience Developmental Cognitive Neuroimaging Suite 17-369 740 Westwood Plaza Los Angeles, CA 90095 Phone: (310)525-0865 Fax: (310)206-5518 Email: jbra...@mednet.ucla.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Editing Parcellations
Dear Freesurfer List I am trying to edit the parcellations using tkmedit, but I am unable to effect the Segmentation Brush label using the Configure Segmentation Brush window. Regardless of my selection, my drawing is labeled "out of bounds". I don;t see an apply button or anything like that, so I assumed simply highlighting the tissue class in the Configuration window would change the brush to my selected label. Is there some step I may be moissing when trying to make a selection? I am using the most up to date version of Freesurfer, and have also tried reverting to older versions, all with no success. Thanks for you your assistance. Best regards, Jennifer Bramen, Ph.D. Assistant Research Neuroscientist David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)525-0865 Fax: (310)206-5518 Email: jbra...@mednet.ucla.edu Campus Mail Code 176919 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cannot execute any freesurfer GUI- Error of failed request:
FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-stable-pub-v4.0.3 Kernel info: Darwin 9.0.0 i386 ___ I recently updated to the newest release of freesurfer because for some reason I was unable to run qdec with 4.0.2. Though it appears that everything is setup exactly as it was before, I cannot execute any of the GUI (tkmedit, tksurfer, or qdec) I tried using the tutorial dataset to debug this. Below is an example command: tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Regardless of what I try to run, I get the following error: Couldn't create output file .xdebug_tkmeditX Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 17 Current serial number in output stream: 17 I already looked in the archives. I do have the most up to date version of X11. I am running this on my local machine, not via ssh, so this is not a display problem. All of my necessary variables are set (SUBJECTS_DIR, FREESURFER_HOME) and I have sourced $FREESURFER_HOME/ SetUpFreeSurfer.csh. Thnaks you in advance for your help. Jennifer Bramen -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] White Matter Regional Volumes
Hi Freesurfer Users, This may be a newbie question. I am trying to evaluate regional volumes. I have been able to tabulate the gray matter volumes, but cannot figure out how to tabulate all the white matter volumes. I see that in individual folders, there is a file called wmparc.stats. Do any of the tools query this file, or will I need to pull the data manually? Inside this file, I see some of the regions listed as wm-?h- . Next to these are sometimes a lot of zeros and sometimes a bunch of values. I am wondering why so many of these do not have values associated with them. I am also wondering why only some of the regions listed in this file are labeled wm, when the file suggests it contains white matter stats... If there is somewhere on the site that explains white matter volumetric analyses, could someone please send me the link? Thank you Jennifer Bramen -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] White Matter Regional Volumes
I posted the below question regarding white matter volumes to the list last Friday. I think it fell through the cracks because I sent it out in the late afternoon, and was hoping someone could help me understand 1) the outputs of indicvidual wmparc.stats files and 2) how to tabulate these data like we can with gray matter volumes. Thanks again. Jen Hi Freesurfer Users, This may be a newbie question. I am trying to evaluate regional volumes. I have been able to tabulate the gray matter volumes, but cannot figure out how to tabulate all the white matter volumes. I see that in individual folders, there is a file called wmparc.stats. Do any of the tools query this file, or will I need to pull the data manually? Inside this file, I see some of the regions listed as wm-? h-. Next to these are sometimes a lot of zeros and sometimes a bunch of values. I am wondering why so many of these do not have values associated with them. I am also wondering why only some of the regions listed in this file are labeled wm, when the file suggests it contains white matter stats... If there is somewhere on the site that explains white matter volumetric analyses, could someone please send me the link? Thank you Jennifer Bramen -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]
External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze amyloid PET data using PETSurfer. I am trying to do kinetic modeling and I am on the MRTM1 step. I have tried this two ways (one using the wiki instructions and the other using the tutorial ROI-based approach) mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/km.hb.tac.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o mrtm1 --no-est-fwhm --nii.gz; done mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/gtm.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o $PET_DIR/PREV_019/mrtm1.roi --nii.gz;done Both times I get this error: error: MatrixReadTxT: could not scan value [1][1] I have opened all of the .dat files using my text editor (nano) and they seem ok. I have tried this in other subjects and I get the same error. I searched the list and I cannot find any discussion regarding this error using mri_glmfit and PET data. Anything you can do to help me troubleshoot this error would be greatly appreciated!!! Attached is my time.dat file (I think this is the most likely culprit). Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center time.dat Description: time.dat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]
External Email - Use Caution Hi Doug I think my first question should be “do I need to do KM?”. This is an amyloid scan and I want to estimate intensity within regions of interest. Do I need KM to estimate mean intensity? This is what I know about the timing of the 4 amyloid PET volumes: 5 min (300 sec) – Amyloid Brain * (5 minx 4 beds) * 40 min uptake * 10 mCi IV injection Can I just create a mean volume from this image or some other simple metric instead of KM? Thanks for your help. Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Friday, February 4, 2022 at 5:09 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1] Can you send all the terminal output? Also, you only have 4 time points in time.dat. Is this accurate? It's going to be hard to do KM with 4 time points. On 1/31/2022 5:00 PM, Jennifer Bramen wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze amyloid PET data using PETSurfer. I am trying to do kinetic modeling and I am on the MRTM1 step. I have tried this two ways (one using the wiki instructions and the other using the tutorial ROI-based approach) mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/km.hb.tac.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o mrtm1 --no-est-fwhm --nii.gz; done mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/gtm.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o $PET_DIR/PREV_019/mrtm1.roi --nii.gz;done Both times I get this error: error: MatrixReadTxT: could not scan value [1][1] I have opened all of the .dat files using my text editor (nano) and they seem ok. I have tried this in other subjects and I get the same error. I searched the list and I cannot find any discussion regarding this error using mri_glmfit and PET data. Anything you can do to help me troubleshoot this error would be greatly appreciated!!! Attached is my time.dat file (I think this is the most likely culprit). Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/10nf2AL62v0JqktSPo3yVbHRsAsxYmB0RqQ4T1KsXIps_k68SFx68P2V_UOWQe-3fgp0LywsEJ_7mKCYxrZliNmu1BADVn8sM86A3NLuueKzBU-_ht-IkzuqZIXLTCrvzzHo4EzvdFGkZI7ao9LFF8ELRRJYgyMTCQzJ8_F-602282DJZWe6e_O6P8qADXfouJVk5CvD2cG5iEf-07ZaNDpvK9voS44YAvwpUbZwoHwxQnbT74BxIlYabrtrJsVULPnjGZgeYz00-98CEf07dh2m-dvKWciq5Z78go6UinOj8LapKpPBgrCbFHmQrbld4OeGXcEUySDxJrpiYUj0gYA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]
External Email - Use Caution Hi Doug I think I figured out my answer. ADNI does 4 volume Amyloid PET analyses by averaging the 4 volumes together. I do not need to do kinetic modeling. I hope this helps someone else in the same situation in the future. Thanks! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 From: on behalf of Jennifer Bramen Reply-To: Freesurfer support list Date: Monday, February 7, 2022 at 9:50 AM To: Freesurfer support list Subject: Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1] External Email - Use Caution Hi Doug I think my first question should be “do I need to do KM?”. This is an amyloid scan and I want to estimate intensity within regions of interest. Do I need KM to estimate mean intensity? This is what I know about the timing of the 4 amyloid PET volumes: 5 min (300 sec) – Amyloid Brain * (5 minx 4 beds) * 40 min uptake * 10 mCi IV injection Can I just create a mean volume from this image or some other simple metric instead of KM? Thanks for your help. Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Friday, February 4, 2022 at 5:09 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1] Can you send all the terminal output? Also, you only have 4 time points in time.dat. Is this accurate? It's going to be hard to do KM with 4 time points. On 1/31/2022 5:00 PM, Jennifer Bramen wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze amyloid PET data using PETSurfer. I am trying to do kinetic modeling and I am on the MRTM1 step. I have tried this two ways (one using the wiki instructions and the other using the tutorial ROI-based approach) mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/km.hb.tac.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o mrtm1 --no-est-fwhm --nii.gz; done mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/gtm.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o $PET_DIR/PREV_019/mrtm1.roi --nii.gz;done Both times I get this error: error: MatrixReadTxT: could not scan value [1][1] I have opened all of the .dat files using my text editor (nano) and they seem ok. I have tried this in other subjects and I get the same error. I searched the list and I cannot find any discussion regarding this error using mri_glmfit and PET data. Anything you can do to help me troubleshoot this error would be greatly appreciated!!! Attached is my time.dat file (I think this is the most likely culprit). Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1eZiIhtszMZEFIQLM5mSk606ezRs_5aImrw_-n253xmwVW2zqRYpuZux-DzbDnp7lXnvb-V3ahiKI26oNpYiBzsIeyzBQswHtxidcQlUR5c0JW20ZquO7r03bCF0lrBZGH5I177ukC5El7g1xmElI6Qt-ER4UHfFhRip9mavSeyePh4a0Zri7S7Gt54fQ3CGzDmjWVj-L7mYjLeO0_t-mz01JOLLjAcHR5eqSS--Vsn5OamziXDBUW0EjnFoFXaSw-cNKER7wxd8y4Qi2tyNAkZlLFApp6OMqsTQFFUZyaMR5yvZ95zfEah9miGrp2BAh/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/10nf2AL62v0JqktSPo3yVbHRsAsxYmB0RqQ4T1KsXIps_k68SFx68P2V_UOWQe-3fgp0LywsEJ_7mKCYxrZliNmu1BADVn8sM86A3NLuueKzBU-_ht-IkzuqZIXLTCrvzzHo4EzvdFGkZI7ao9LFF8ELRRJYgyMTCQzJ8_F-602282DJZWe6e_O6P8qADXfouJVk5CvD2cG5iEf-07ZaNDpvK9voS44YAvwpUbZwoHwxQnbT74BxIlYabrtrJsVULPnjGZgeYz00-98CEf07dh2m-dvKWciq5Z78go6UinOj8LapKpPBgrCbFHmQrbld4OeGXcEUySDxJrpiYUj0gYA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] PetSurfer: subcortical volume-based analysis
External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I have completed all of the steps from the PetSurfer wiki. I now have the preprocessed, averaged, resampled, smoothed PET data in MNI305 space which is constrained to the subcortical gray matter mask. How do I extract mean intensity within all of the subcortical ROI? Thank you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] PetSurfer: CORTICAL volume-based analysis
External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I am following the steps from the PetSurfer wiki. I see instructions for how to do a cortical surface-based group analysis. I also see how to do a subcortical ROI-based analysis. However, I cannot find detailed instructions for performing a cortical ROI-based analysis. This is how I think I should adapt the instructions from your subcortical ROI-based analysis instructions for cortical gray matter: mri_vol2vol --mov $PET_DIR/$ID/gtmpvc.output/mgx.gm.nii.gz --reg $PET_DIR/$ID/gtmpvc.output/aux/bbpet2anat.lta --tal --talres 2 --o $PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz mri_fwhm --smooth-only --i $PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz --fwhm 5 --o $PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm05.nii.gz --mask $FREESURFER_HOME/subjects/fsaverage/mri.2mm/brainmask.mgz Can someone confirm or correct these commands? I am especially concerned that I have selected the wrong mask. Thanks you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
External Email - Use Caution I am trying to extract mean intensity in my PET data for every ROI. Doug said to run mri_segstats passing the PET with --i and using --seg to spec the segmentation. I would like to confirm that I am using this properly. mri_segstats --i $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg $SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum $PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the PET data registered and resampled into the individual’s T1-weighrd MRI space. Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Wednesday, February 16, 2022 at 7:30 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis If you want to do an ROI analysis using FS-based ROIs, you should do that at the individual level. Resample the PET to the anatoimical space, then run mri_segstats passing the PET with --i and using --seg to spec the segmentation. If you really want to do it in MNI305 space, then it is the same thing just using the MNI305-based (2mm) segmentation On 2/14/2022 6:11 PM, Jennifer Bramen wrote: External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I have completed all of the steps from the PetSurfer wiki. I now have the preprocessed, averaged, resampled, smoothed PET data in MNI305 space which is constrained to the subcortical gray matter mask. How do I extract mean intensity within all of the subcortical ROI? Thank you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1pHRKHdySejszKCsrs9a5H_HhNUL-CC5YeU4Cl_81vNtgCRYphxx1lXfNUS28oh3w1R-TndgZ47wOf2XFHWg3dBsYow738wDFOOYfSwGLuBCjeJ-FaIOQPsyai7IAeZ1dOxsmP6GuyW5j2bVWEFjAU09qZ4M9zHUa2XyfmlPf4piiqQbo3Ayz3gL78M-vcSa8d1BpjLa9zF3PA4aHAuzSSyumGTLdIAY-5_L_6XgNw7iEG5NYmI7TPk5Phat5eGYdipePAy6m0hB1ibRYO0p1h0wvZVeul211fN1oB8Pwq1PTrPMjeCu2cTqbID6R2Q-DwaPaMHuhE_4IcMArFhh63A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
External Email - Use Caution Thanks! Yes, I already mapped my PET to anatomical space using mri_vol2vol and glmdir/aux/bbpet2anat.lta. RE: selection of mgx instead of gtm: I am analyzing amyloid PET data and I believe it is recommended to extract gray matter localized PET data. Is that what I am doing by using the mgx image? Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Monday, February 21, 2022 at 2:02 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis You need to first map your pet to the anatomical space using mri_vol2vol and the registration glmdir/aux/bbpet2anat.lta BTW, why are you computing the ROI anlaysis from the mgx data instead of using the output from the gtm? Note that you cannot use the white matter values that come from mgx. On 2/21/2022 12:57 PM, Jennifer Bramen wrote: External Email - Use Caution I am trying to extract mean intensity in my PET data for every ROI. Doug said to run mri_segstats passing the PET with --i and using --seg to spec the segmentation. I would like to confirm that I am using this properly. mri_segstats --i $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg $SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum $PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the PET data registered and resampled into the individual’s T1-weighrd MRI space. Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, February 16, 2022 at 7:30 AM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis If you want to do an ROI analysis using FS-based ROIs, you should do that at the individual level. Resample the PET to the anatoimical space, then run mri_segstats passing the PET with --i and using --seg to spec the segmentation. If you really want to do it in MNI305 space, then it is the same thing just using the MNI305-based (2mm) segmentation On 2/14/2022 6:11 PM, Jennifer Bramen wrote: External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I have completed all of the steps from the PetSurfer wiki. I now have the preprocessed, averaged, resampled, smoothed PET data in MNI305 space which is constrained to the subcortical gray matter mask. How do I extract mean intensity within all of the subcortical ROI? Thank you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/183gHoF2QNWF0XhiYjGNXYG6PPLdbxs7KNgXhQsXHho8xZeK39atN7Jo6IrguyAfg0UBKyIPPcrj8etGhWOIJSNajPkkOaei1R60Wd4bPE580iHNNu_GQG7BBenVzhSh8t2VkqrI4Q6QSCRZqq2EjampfrVY983C-QNTmp78vE1y84HS6yv0YGhl-4D3SbUFqsLCBh2IkABxx72wmJE7GCNlYMkb8ZLiJ_ycvg1ZLF_XkTN4RELwpHwjAuhJ0UJqGWFCl4wzrgr5imnM5q5gpOYtuSlA1riTYcmWbehUIE8csYd3C-9XHdR01xyYX-Prz/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1pHRKHdySejszKCsrs9a5H_HhNUL-CC5YeU4Cl_81vNtgCRYphxx1lXfNUS28oh3w1R-TndgZ47wOf2XFHWg3dBsYow738wDFOOYfSwGLuBCjeJ-FaIOQPsyai7IAeZ1dOxsmP6GuyW5j2bVWEFjAU09qZ4M9zHUa2XyfmlPf4piiqQbo3Ayz3gL78M-vcSa8d1BpjLa9zF3PA4aHAuzSSyumGTLdIAY-5_L_6XgNw7iEG5NYmI7TPk5Phat5eGYdipePAy6m0hB1ibRYO0p1h0wvZVeul211fN1oB8Pwq1PTrPMjeCu2cTqbID6R2Q-DwaPaMHuhE_4IcMArFhh63A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> ___ Frees
Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
External Email - Use Caution If I only want to extract intensity from gray matter, do I need to add an additional mask? Thanks! Jennifer Get Outlook for iOS<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Monday, February 21, 2022 7:13:39 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis The GTM gives you values for each ROI regardless of whether it is GM, WM, or CSF. They will probably give you similar answers, but the GTM will be more robust. On 2/21/2022 8:48 PM, Jennifer Bramen wrote: External Email - Use Caution Thanks! Yes, I already mapped my PET to anatomical space using mri_vol2vol and glmdir/aux/bbpet2anat.lta. RE: selection of mgx instead of gtm: I am analyzing amyloid PET data and I believe it is recommended to extract gray matter localized PET data. Is that what I am doing by using the mgx image? Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, February 21, 2022 at 2:02 PM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis You need to first map your pet to the anatomical space using mri_vol2vol and the registration glmdir/aux/bbpet2anat.lta BTW, why are you computing the ROI anlaysis from the mgx data instead of using the output from the gtm? Note that you cannot use the white matter values that come from mgx. On 2/21/2022 12:57 PM, Jennifer Bramen wrote: External Email - Use Caution I am trying to extract mean intensity in my PET data for every ROI. Doug said to run mri_segstats passing the PET with --i and using --seg to spec the segmentation. I would like to confirm that I am using this properly. mri_segstats --i $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg $SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum $PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the PET data registered and resampled into the individual’s T1-weighrd MRI space. Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, February 16, 2022 at 7:30 AM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis If you want to do an ROI analysis using FS-based ROIs, you should do that at the individual level. Resample the PET to the anatoimical space, then run mri_segstats passing the PET with --i and using --seg to spec the segmentation. If you really want to do it in MNI305 space, then it is the same thing just using the MNI305-based (2mm) segmentation On 2/14/2022 6:11 PM, Jennifer Bramen wrote: External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I have completed all of the steps from the PetSurfer wiki. I now have the preprocessed, averaged, resampled, smoothed PET data in MNI305 space which is constrained to the subcortical gray matter mask. How do I extract mean intensity within all of the subcortical ROI? Thank you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Founda
Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
External Email - Use Caution I would like to measure uptake exclusively in gray matter. What would you recommend to accomplish this? In my previous message, I was wondering if adding a gray matter mask would be a potential way to restrict the analysis to gray matter. Thanks! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Tuesday, February 22, 2022 at 3:00 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis I don't understand. What mask? On 2/22/2022 8:55 AM, Jennifer Bramen wrote: External Email - Use Caution If I only want to extract intensity from gray matter, do I need to add an additional mask? Thanks! Jennifer Get Outlook for iOS<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef> From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <mailto:dgr...@mgh.harvard.edu> Sent: Monday, February 21, 2022 7:13:39 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis The GTM gives you values for each ROI regardless of whether it is GM, WM, or CSF. They will probably give you similar answers, but the GTM will be more robust. On 2/21/2022 8:48 PM, Jennifer Bramen wrote: External Email - Use Caution Thanks! Yes, I already mapped my PET to anatomical space using mri_vol2vol and glmdir/aux/bbpet2anat.lta. RE: selection of mgx instead of gtm: I am analyzing amyloid PET data and I believe it is recommended to extract gray matter localized PET data. Is that what I am doing by using the mgx image? Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, February 21, 2022 at 2:02 PM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis You need to first map your pet to the anatomical space using mri_vol2vol and the registration glmdir/aux/bbpet2anat.lta BTW, why are you computing the ROI anlaysis from the mgx data instead of using the output from the gtm? Note that you cannot use the white matter values that come from mgx. On 2/21/2022 12:57 PM, Jennifer Bramen wrote: External Email - Use Caution I am trying to extract mean intensity in my PET data for every ROI. Doug said to run mri_segstats passing the PET with --i and using --seg to spec the segmentation. I would like to confirm that I am using this properly. mri_segstats --i $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg $SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum $PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the PET data registered and resampled into the individual’s T1-weighrd MRI space. Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, February 16, 2022 at 7:30 AM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:f
Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
External Email - Use Caution Hi Doug I want to confirm that the signal any region flagged as cortex is restricted to gray matter. If that is the case, then I finally have what I need. Thank you. Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Friday, February 25, 2022 at 10:25 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis Are you doing an ROI analysis or a voxel-wise analysis? If an ROI analysis, then use mri_gtmpvc (with or without PVC). This will give you GM, WM, and CSF ROIs. Or do you mean you want a single average across all GM? On 2/24/2022 1:15 PM, Jennifer Bramen wrote: External Email - Use Caution I would like to measure uptake exclusively in gray matter. What would you recommend to accomplish this? In my previous message, I was wondering if adding a gray matter mask would be a potential way to restrict the analysis to gray matter. Thanks! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, February 22, 2022 at 3:00 PM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis I don't understand. What mask? On 2/22/2022 8:55 AM, Jennifer Bramen wrote: External Email - Use Caution If I only want to extract intensity from gray matter, do I need to add an additional mask? Thanks! Jennifer Get Outlook for iOS<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef> From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <mailto:dgr...@mgh.harvard.edu> Sent: Monday, February 21, 2022 7:13:39 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis The GTM gives you values for each ROI regardless of whether it is GM, WM, or CSF. They will probably give you similar answers, but the GTM will be more robust. On 2/21/2022 8:48 PM, Jennifer Bramen wrote: External Email - Use Caution Thanks! Yes, I already mapped my PET to anatomical space using mri_vol2vol and glmdir/aux/bbpet2anat.lta. RE: selection of mgx instead of gtm: I am analyzing amyloid PET data and I believe it is recommended to extract gray matter localized PET data. Is that what I am doing by using the mgx image? Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, February 21, 2022 at 2:02 PM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis You need to first map your pet to the anatomical space using mri_vol2vol and the registration glmdir/aux/bbpet2anat.lta BTW, why are you computing the ROI anlaysis from the mgx data instead of using the output from the gtm? Note that you cannot use the white matter values that come from mgx. On 2/21/2022 12:57 PM, Jennifer Bram
[Freesurfer] mri_convert and timeseries data
Dear Freesurfer Users I am trying to use mri_convert to reorient a nifti file. The file is a bold sequence, but for some reason, mri_convert is only outputting the first volume. I get this error as well: WARNING: niiRead(): unknown time units 0 in 2010_10_20_21_bold_gp2.nii Any idea regarding what I am doing wrong? Here is the command I used: mri_convert --in_orientation SLP --out_orientation LPI 2010_10_20_21_bold_gp2.nii 2010_10_20_21_bold_gp_RPI2.nii Any help would be greatly appreciated! Best regards Jen ___ 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.
