[Freesurfer] Partial volume correction for intensity sampling
Hi, Is there a way to address or account the effects of partial voluming when sampling grey matter intensity (mri_vol2surf)? In particular, where there is cortical thinning, I'm also finding intensity changes that could either be due to changes in the amount of partial voluming or a change in the grey matter tissue contrast. Is there any way to disambiguate the two? The commands I'm using are: bbregister --s $s --mov $s --mov $s/mri/brainmask.mgz --reg $s/mri/transforms/Identity.dat --init-fsl --t1 mri_vol2surf --src $s/mri/brainmask.mgz --out $s/surf/$h.T1_intensity.mgh --srcreg $s/mri/transforms/Identity.dat --hemi $h --projfrac 0.2 Thanks, Konrad ___ 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] isxconcat-sess without fsaverage
I put it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess If you just want to concatenate the vertex values, then just do something like mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz sess2/bold/analysis/contrast/ces.nii.gz ... On 04/27/2015 02:28 PM, Reza Rajimehr wrote: Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com mailto:rajim...@gmail.com wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ 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] GLM_ functional connectivity analysis
can you send the two command lines you ran? On 04/27/2015 02:53 PM, Alshikho, Mohamad J. wrote: Hi Doug, I am working on a GLM for functional connectivity analysis. I made simple FSGD file for two groups + NO covariates then I ran the following command line on the right hemisphere and the left hemisphere. mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd fsgd --C Contrast1group.diff.mtx --C Contrast2group1.mtx --C Contrast3group2.mtx --C Contrast4g1g2.intercept.mtx --surface fsaverage lh --glmdir glm-fsgd-2G0C.wls --nii.gz On the right hemisphere the output is fine for all the contrasts. On the left hemisphere and after writing the results for contrast 1 I am receiving the following message: MatrixMultiply: m2 is null! Kindly what is the meaning of this message? Thanks, Mohamad ___ 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] isxconcat-sess without fsaverage
You can mri_concat the cesvar files. For the dof, just add up the dofs in each run. On 04/27/2015 05:08 PM, Reza Rajimehr wrote: If I use mri_concat instead of isxconcat-sess, will I have all the necessary files for fixed-effects averaging by mri_glmfit? Specifically, can I generate cesvar.nii for --yffxvar and ffxdof.dat for --ffxdofdat in mri_glmfit? Reza I put it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess If you just want to concatenate the vertex values, then just do something like mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz sess2/bold/analysis/contrast/ces.nii.gz ... On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com mailto:rajim...@gmail.com wrote: Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com javascript:_e(%7B%7D,'cvml','rajim...@gmail.com'); wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ 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] isxconcat-sess without fsaverage
If I use mri_concat instead of isxconcat-sess, will I have all the necessary files for fixed-effects averaging by mri_glmfit? Specifically, can I generate cesvar.nii for --yffxvar and ffxdof.dat for --ffxdofdat in mri_glmfit? Reza I put it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess If you just want to concatenate the vertex values, then just do something like mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz sess2/bold/analysis/contrast/ces.nii.gz ... On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote: Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com javascript:_e(%7B%7D,'cvml','rajim...@gmail.com'); wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ 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] GLM_ functional connectivity analysis
I ran only one command line : mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd fsgd --C Contrast1group.diff.mtx --C Contrast2group1.mtx --C Contrast3group2.mtx --C Contrast4g1g2.intercept.mtx --surface fsaverage lh --glmdir glm-fsgd-2G0C.wls --nii.gz This command ran smoothly on the right hemisphere so I ran the second command : mri_glmfit-sim --glmdir glm-fsgd-2G0C.wls --cache 3 pos --cwpvalthresh 0.166 But when I run the first command line on the left hemisphere using the same FSGD file and the same contrast I receive the following message : INFO: gd2mtx_method is dods Saving design matrix to glm-fsgd-2G0C.wls/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 2.5 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 148773 voxels in mask Saving mask to glm-fsgd-2G0C.wls/mask.nii.gz Reshaping mriglm-mask... search space = 74067.765554 DOF = 12 Starting fit and test Fit completed in 0.115333 minutes Computing spatial AR1 on surface WARNING: ar1 = 0 = 0. Setting fwhm to 0. Residual: ar1mn=0.00, ar1std=0.00, gstd=0.00, fwhm=0.00 Writing results Contrast1group.diff maxvox sig=1e+10 F=0 at index 204 0 0seed=1430655459 MatrixMultiply: m2 is null! I can't figure out what is the meaning what is the message From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, April 27, 2015 4:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM_ functional connectivity analysis can you send the two command lines you ran? On 04/27/2015 02:53 PM, Alshikho, Mohamad J. wrote: Hi Doug, I am working on a GLM for functional connectivity analysis. I made simple FSGD file for two groups + NO covariates then I ran the following command line on the right hemisphere and the left hemisphere. mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd fsgd --C Contrast1group.diff.mtx --C Contrast2group1.mtx --C Contrast3group2.mtx --C Contrast4g1g2.intercept.mtx --surface fsaverage lh --glmdir glm-fsgd-2G0C.wls --nii.gz On the right hemisphere the output is fine for all the contrasts. On the left hemisphere and after writing the results for contrast 1 I am receiving the following message: MatrixMultiply: m2 is null! Kindly what is the meaning of this message? Thanks, Mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Edits to longitudinal pial surface and aseg
Hi, editing the long does not really introduce much bias I think. It is usually not necessary and it is not recommended, because often it problems in the long are caused by earlier problems in the base or even cross, so it is best to fix it there. Your case seems to be different (problems first occur in long). I would try in one case if editing the long works in your situation. It sounds like it should. Best, Martin On 04/22/2015 08:14 PM, prasser wrote: Repost. Thanks. On Mon, 20 Apr 2015 16:21:38 -0700 *pras...@zoho.com* wrote Thank you for your reply. Yes, I'm finding that it is only small edits that are required in the Long for the case of pial surface errors. It is usually in areas where no editing was required in the cross and base, but the pial surface in the Long extends to include dura or cerebellum. I was hoping just to edit the Long brainmask.mgz and brain.finalsurfs.manedit.mgz and re-run with the command recon-all -long tpN1 templateID -autorecon2-pial -autorecon3 and then re-check the surfaces. The alternative as I see it would be 1. Identify the corresponding locations in the Base (even though it is not a problem in the Base) 2. edit, re-run and re-check the Base 3. delete, create and check all new Longs This second option would take a considerable amount of time and may not solve the problem in one iteration. I'm guessing the concerns with the first method are introducing bias any other concerns with editing the Long? P On Mon, 20 Apr 2015 12:21:51 -0700 *Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu* wrote Hi P, usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfer.net/fswiki/LongitudinalEdits for a description of the different edits, and where they should be done. About where to restart after making the edits, everything should be done the same way as in the regular (cross sectional) processing. So you specifically ask about: - brainmask edits - brainfinalsurf edits - and manual aseg edits. I just looked at the description of those regular edits http://freesurfer.net/fswiki/Edits but sadly there it does not say where to start re-run either. I'll try to find out and update that soon. I hope someone with editing experience can chime in and tell us. (I changed the subject, so that it get's read). Cheers, Martin On 04/20/2015 09:44 AM, Bruce Fischl wrote: cheers Bruce On Mon, 20 Apr 2015, prasser wrote: Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email:mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu reu...@mit.edu mailto:reu...@mit.edu Web :http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] Partial volume correction for intensity sampling
Hi Konrad if you read Rebecca Shafee's recent paper: http://www.ncbi.nlm.nih.gov/pubmed/25449739 you can see what we do about this kind of thing. The stream is largely undocumented but you are welcome to try it out if you like. cheers Bruce On Mon, 27 Apr 2015, K. Wagstyl wrote: Hi, Is there a way to address or account the effects of partial voluming when sampling grey matter intensity (mri_vol2surf)? In particular, where there is cortical thinning, I'm also finding intensity changes that could either be due to changes in the amount of partial voluming or a change in the grey matter tissue contrast. Is there any way to disambiguate the two? The commands I'm using are: bbregister --s $s --mov $s --mov $s/mri/brainmask.mgz --reg $s/mri/transforms/Identity.dat --init-fsl --t1 mri_vol2surf --src $s/mri/brainmask.mgz --out $s/surf/$h.T1_intensity.mgh --srcreg $s/mri/transforms/Identity.dat --hemi $h --projfrac 0.2 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] Partial volume correction for intensity sampling
Hi Bruce, Thanks for this. I did see this paper and would like to try the correction method - is it included in a new release of freesurfer or is it a separate script? If it's separate, would it be possible to try it? Many thanks, Konrad On 2015-04-27 13:43, Bruce Fischl wrote: Hi Konrad if you read Rebecca Shafee's recent paper: http://www.ncbi.nlm.nih.gov/pubmed/25449739 you can see what we do about this kind of thing. The stream is largely undocumented but you are welcome to try it out if you like. cheers Bruce On Mon, 27 Apr 2015, K. Wagstyl wrote: Hi, Is there a way to address or account the effects of partial voluming when sampling grey matter intensity (mri_vol2surf)? In particular, where there is cortical thinning, I'm also finding intensity changes that could either be due to changes in the amount of partial voluming or a change in the grey matter tissue contrast. Is there any way to disambiguate the two? The commands I'm using are: bbregister --s $s --mov $s --mov $s/mri/brainmask.mgz --reg $s/mri/transforms/Identity.dat --init-fsl --t1 mri_vol2surf --src $s/mri/brainmask.mgz --out $s/surf/$h.T1_intensity.mgh --srcreg $s/mri/transforms/Identity.dat --hemi $h --projfrac 0.2 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] isxconcat-sess without fsaverage
Thanks Doug! Could you clarify a bit more on how to add up the dofs in each run? You can mri_concat the cesvar files. For the dof, just add up the dofs in each run. On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote: If I use mri_concat instead of isxconcat-sess, will I have all the necessary files for fixed-effects averaging by mri_glmfit? Specifically, can I generate cesvar.nii for --yffxvar and ffxdof.dat for --ffxdofdat in mri_glmfit? Reza I put it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess If you just want to concatenate the vertex values, then just do something like mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz sess2/bold/analysis/contrast/ces.nii.gz ... On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com javascript:_e(%7B%7D,'cvml','rajim...@gmail.com'); wrote: Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ 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] isxconcat-sess without fsaverage
Eachoutput.nii.gz sess1/bold/analysis folder will have a dof.dat file with a number in it. Add up all those numbers, create a files with the sum in it, and pass that file to mrI_gomfit. On 04/27/2015 06:18 PM, Reza Rajimehr wrote: Thanks Doug! Could you clarify a bit more on how to add up the dofs in each run? You can mri_concat the cesvar files. For the dof, just add up the dofs in each run. On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com mailto:rajim...@gmail.com wrote: If I use mri_concat instead of isxconcat-sess, will I have all the necessary files for fixed-effects averaging by mri_glmfit? Specifically, can I generate cesvar.nii for --yffxvar and ffxdof.dat for --ffxdofdat in mri_glmfit? Reza I put it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess If you just want to concatenate the vertex values, then just do something like mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz sess2/bold/analysis/contrast/ces.nii.gz ... On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com javascript:_e(%7B%7D,'cvml','rajim...@gmail.com'); wrote: Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ 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] GLM_ functional connectivity analysis
Hi Doug, I am working on a GLM for functional connectivity analysis. I made simple FSGD file for two groups + NO covariates then I ran the following command line on the right hemisphere and the left hemisphere. mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd fsgd --C Contrast1group.diff.mtx --C Contrast2group1.mtx --C Contrast3group2.mtx --C Contrast4g1g2.intercept.mtx --surface fsaverage lh --glmdir glm-fsgd-2G0C.wls --nii.gz On the right hemisphere the output is fine for all the contrasts. On the left hemisphere and after writing the results for contrast 1 I am receiving the following message: MatrixMultiply: m2 is null! Kindly what is the meaning of this message? Thanks, Mohamad ___ 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] isxconcat-sess without fsaverage
Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ 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.
