Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat
Thanks Doug! One last question: If I wanted to regress out the average signal from the ventricles and the white matter (instead of using the PCA output), could I directly incorporate that into fcseedcor? Best, Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve Sent: Friday, July 20, 2018 9:23:58 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat Hi Hamdi, sorry for the delay. Answers below. On 6/26/18 2:50 PM, Eryilmaz, H. Hamdi wrote: Hi Doug and Freesurfers, I am using fcseedcor to compute the correlation between two time courses for each subject in my group. The command that I run is as follows: fcseedcor -s $subject -fsd resting -seed seed1.dat -seed seed2.dat -xreg global.waveform.dat 1 -xreg vcsf.dat 5 -xreg wm.dat 5 -xreg mcprextreg 6 -hpf .01 -lpf .08 -nskip 4 -o cor_s1s2.dat My first question is about the size of the vcsf.dat and wm.dat files. They seem to be (N+1)xN matrices, where N is the number of timepoints in the signal. Does this mean there are N+1 components for each time point (i.e., N+1 potential regressors to add)? What do they exactly correspond to and how do they relate to the average signal from the ventricles, CSF, and white matter? Each ROI consists of a matrix of size Ntp-by-Nvoxels. A PCA is computed from this matrix. The the number of temporal components of the PCA will be either Ntp or Nvoxels, which ever is less. In this case, Nvoxels>Ntp, so you see the Ntp components (each Ntp long). The components are whatever the PCA finds. The mean is removed, so it no component represents the mean. My other question is about the number of components to include for vcsf.dat and wm.dat. I have seen 5 recommended in examples, however, five components seem to explain very different amount of variance in different subjects and if I change this number for a given subject, I see substantial changes in the resulting correlation value. I would appreciate any suggestion on how to select an unbiased value for the number of components to include. Could including up to the component at which fixed percentage of cumulative variance is explained be a solution? When I was doing experiments with this years ago, i did not find much of a difference with different numbers of components, but I did the experiments on whole brain resting state, so the ROI-wise correlation may be different. It seemed like 5 components explained the bulk of the variance within the ROI (WM or CSF). You could vary the number of components for each subject. Sorry, I don't have any better guidance on how to go about selecting the number. doug Many thanks for your help! Best, Hamdi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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] fcseedcor -- pca output for vcsf.dat and wm.dat
Hi Doug and Freesurfers, I am using fcseedcor to compute the correlation between two time courses for each subject in my group. The command that I run is as follows: fcseedcor -s $subject -fsd resting -seed seed1.dat -seed seed2.dat -xreg global.waveform.dat 1 -xreg vcsf.dat 5 -xreg wm.dat 5 -xreg mcprextreg 6 -hpf .01 -lpf .08 -nskip 4 -o cor_s1s2.dat My first question is about the size of the vcsf.dat and wm.dat files. They seem to be (N+1)xN matrices, where N is the number of timepoints in the signal. Does this mean there are N+1 components for each time point (i.e., N+1 potential regressors to add)? What do they exactly correspond to and how do they relate to the average signal from the ventricles, CSF, and white matter? My other question is about the number of components to include for vcsf.dat and wm.dat. I have seen 5 recommended in examples, however, five components seem to explain very different amount of variance in different subjects and if I change this number for a given subject, I see substantial changes in the resulting correlation value. I would appreciate any suggestion on how to select an unbiased value for the number of components to include. Could including up to the component at which fixed percentage of cumulative variance is explained be a solution? Many thanks for your help! Best, Hamdi ___ 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] connectivity between two ROIs
Dear all, I would like to use the fsfast functional connectivity pipeline to compute connectivity between two binarized ROIs. One of the ROIs is a surface ROI, the other is a hippocampal subfield. Based on the tutorial on http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough, I created the time courses for the two ROIs. However, in order to regress out the signal from the ventricles, CSF, and white matter as well as the motion parameters, it seems that I need to run a whole-brain analysis (or at least one hemisphere). Is that correct? Would it be possible to compute connectivity just between two given ROIs without needing to run the analysis on the hemisphere? Thanks a lot! Best, Hamdi ___ 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] visualizing seeds on surface
Hi Doug, They are in MNI but I can find out their vertex numbers if that would be easier. Thanks! Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Wednesday, May 2, 2018 5:42:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] visualizing seeds on surface What coordinate system are the seed coordinates in? Do you know the vertex number on the surface? On 05/02/2018 03:13 PM, Eryilmaz, H. Hamdi wrote: > > Dear freeview experts, > > Is it possible to display multiple seeds (i.e., as a small circle) on > freeview surface view by specifying their coordinates? If there is no > such feature, could you suggest an alternative way to visualize seeds? > > Thanks in advance! > > Best, > Hamdi > > > > > ___ > 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.
[Freesurfer] visualizing seeds on surface
Dear freeview experts, Is it possible to display multiple seeds (i.e., as a small circle) on freeview surface view by specifying their coordinates? If there is no such feature, could you suggest an alternative way to visualize seeds? Thanks in advance! Best, Hamdi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] smoothing a surface map
Hello all, How can I simply smooth a surface map (constructed using MRIwrite) using a specific FWHM? mri_surf2surf requires source subject as an input but all I want to do is to smooth a single group map. Thanks in advance for your help! Best, Hamdi ___ 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] modeling thickness data at a given age
Dear all, We are modeling changes in cortical thickness over time using a cross-sectional design. We have two groups of participants, age 8 to 18. In the cortical regions that interest us, there is generally a linear decline in thickness with age. Each group can be fitted to a best-fit line. The question we are interested in is whether there is a significant difference in thickness between groups at a given age (i.e., not just collapsed across age) — specifically, at the earliest age point (age=8). Is this possible to model across the brain surface in Freesurfer? Thanks, Hamdi and Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] white matter ROI mask using an fsaverage label
Hi Anastasia and FS experts, I am trying to create a white matter ROI mask underneath a cortical ROI label (e.g., 2 mm into the white matter) created in fsaverage space. I will then use this mask to extract values from individual dtifit_FA and dtifit_MD maps generated by trac-all. What would be the easiest way to do this? I thought about using mri_aparc2aseg but I am not quite sure about how to specify a label with this command. Thanks so much for your help! Best, Hamdi ___ 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] complement of a label
Dear FreeSurfers, I was wondering if there is a standardized way to construct a label that is the complement of a regional label on freesurfer. For example, I have a customized DLPFC label and would like to create another label that encompasses the entire cortex except that DLPFC region. Thanks for your help. Best, Hamdi ___ 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] group by age-squared interaction on thickness
Dear Doug/FreeSurfers, We are looking at effects of age-squared on cortical thickness in two different groups. We are interested in age-squared by group interactions on cortical thickness across the surface. Nuisance covariates include age, sex, scanner, and total brain volume. The sig map for the interaction shows numerous highly significant regions. When we extract cortical thickness from individual subjects for these regions, and then plot the relationship between age-squared and cortical thickness (after adjusting for the covariates) in group 1 versus group 2, the interaction is very clear. However, using linear regression in SPSS, we are not able to reproduce these results. I suspect we are not using the same model in SPSS that FreeSurfer is using to do the interaction analysis. This is how our fsgd file looks like: GroupDescriptorFile 1 Title GroupAgesqInteraction Class Group1 Class Group2 Variables Agesq Age Gender Scanner TBV Input3662291Group10.6070.654-1.0611.0410.706 Input3665043Group11.2941.237-1.0611.041-0.747 . . This is the contrast we used: [0 0 1 -1 0 0 0 0 0 0 0 0] What would be the translation of this contrast to a linear model, where we are interested in the age -squared by group interaction on cortical thickness after controlling for the four nuisance covariates? Thanks very much! Hamdi and Josh ___ 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] BrainSegVolNotVent
Hi Doug, Thanks for your reply. I just sent you this subject's directory via file drop. Please note that there are two aseg.stats files under the 'stats' folder: aseg.stats: generated by the mri_segstats command I ran including the --brainmask mri/brainmask.mgz --brain-vol-from-seg flags. aseg_original.stats: generated by the original recon-all command. Let me know if you need anything else. Best, Hamdi 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, July 18, 2016 1:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] BrainSegVolNotVent That does look suspicious, esp since BrainSegNotVent should be smaller than BrainSeg. Can you tar up the subject and send it to me? It may be some strange incompatibility with v5 On 07/07/2016 03:50 PM, Eryilmaz, H. Hamdi wrote: > Hello Doug and Freesurfers, > > I am trying to compute a structural measure called > 'BrainSegVolNotVent' as an approximate value of total brain volume. > 'BrainSegVolNotVent' is now present in aseg.stats files but the > dataset I'm working on was preprocessed using FS 5.0, which did not > produce this variable. Per your advice I found in a previous email, I > reran mri_segstats adding the flags --brainmask mri/brainmask.mgz > --brain-vol-from-seg. > > The new aseg.stats file contains the following lines that were added > after running this command: > > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, > 1667093, unitless > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1667093.00, mm^3 > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation > Volume Without Ventricles, 232145.00, mm^3 > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, > 1410666, unitless > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, > 1410666.00, mm^3 > > The numbers look a bit odd. BrainSegVol and BrainSegVolNotVent should > normally be close to each other, right? Also unitless values such as > BrainSegNVox and BrainMaskNVox seem to be equal to their corresponding > volumetric values. > > Do you have any idea what might have gone wrong? Here's the command I > ran: > > mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv > mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent > --subcortgray --in mri/norm.mgz --in-intensity-name norm > --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol > --totalgray --ctab /usr/local/freesurfer/stable5_0_0/ASegStatsLUT.txt > --subject SUBJECT_ID --brainmask mri/brainmask.mgz --brain-vol-from-seg > > > Thanks very much for your help! > > Best, > Hamdi > > > > > > ___ > 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] aparcstats2table -- extracting multiple measures
Hi Doug, I get the following error when I use 'foldind' in this command >> aparcstats2table --hemi lh --subjectsfile $SUBJECTS_DIR/RPDR/214_PrePostFort_FSGDorder --parc rostralmiddlefrontal.label --meas foldind --tablefile $SUBJECTS_DIR/Tables/LH_rostralmiddlefrontal_FoldInd.txt aparcstats2table: error: option --measure: invalid choice: 'foldind' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv') Isn't it an option for aparcstats2table yet? Should I make a matlab or python script to extract it? Thanks! Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, November 13, 2015 6:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures Use foldind On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote: > Thanks Doug for the quick reply! Is there an option in aparcstats2table that > allows to make a table with the folding index measure? If so, what variable > should I use in the flag -meas? > > Best, > Hamdi > > > > 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: Thursday, November 12, 2015 11:26 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures > > you have to run it separately > > On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote: >> Dear experts, >> >> I am using aparcstats2table to extract values on a number of measures >> like thickness, curvature, folding index, and surface area for >> specific ROIs. Is it possible to create a table (using >> aparcstats2table) with all these measures included or do I have to >> run it separately and create a separate table for each measure? >> Passing --meas flag multiple items did not work. >> >> Thanks for your help! >> Hamdi >> >> >> >> >> >> >> ___ >> 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 > > ___ 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] aparcstats2table -- extracting multiple measures
I'm using 5.0. It's a version issue then. Thanks Doug! 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, November 16, 2015 12:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures what version of FS are you using? When I run aparcstats2table --hemi lh -s subject --meas foldind --tablefile table.dat it runs fine On 11/16/2015 10:24 AM, Eryilmaz, H. Hamdi wrote: > Hi Doug, > > I get the following error when I use 'foldind' in this command >> > aparcstats2table --hemi lh --subjectsfile > $SUBJECTS_DIR/RPDR/214_PrePostFort_FSGDorder --parc > rostralmiddlefrontal.label --meas foldind --tablefile > $SUBJECTS_DIR/Tables/LH_rostralmiddlefrontal_FoldInd.txt > > aparcstats2table: error: option --measure: invalid choice: 'foldind' (choose > from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv') > > Isn't it an option for aparcstats2table yet? Should I make a matlab or python > script to extract it? > > Thanks! > Hamdi > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, November 13, 2015 6:27 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures > > Use foldind > > > On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote: >> Thanks Doug for the quick reply! Is there an option in aparcstats2table that >> allows to make a table with the folding index measure? If so, what variable >> should I use in the flag -meas? >> >> Best, >> Hamdi >> >> >> >> 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: Thursday, November 12, 2015 11:26 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures >> >> you have to run it separately >> >> On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote: >>> Dear experts, >>> >>> I am using aparcstats2table to extract values on a number of measures >>> like thickness, curvature, folding index, and surface area for >>> specific ROIs. Is it possible to create a table (using >>> aparcstats2table) with all these measures included or do I have to >>> run it separately and create a separate table for each measure? >>> Passing --meas flag multiple items did not work. >>> >>> Thanks for your help! >>> Hamdi >>> >>> >>> >>> >>> >>> >>> ___ >>> 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 >> >> > ___ > 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 > > -- 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 Free
Re: [Freesurfer] aparcstats2table -- extracting multiple measures
Thanks Doug for the quick reply! Is there an option in aparcstats2table that allows to make a table with the folding index measure? If so, what variable should I use in the flag -meas? Best, Hamdi 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: Thursday, November 12, 2015 11:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures you have to run it separately On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote: > Dear experts, > > I am using aparcstats2table to extract values on a number of measures > like thickness, curvature, folding index, and surface area for > specific ROIs. Is it possible to create a table (using > aparcstats2table) with all these measures included or do I have to > run it separately and create a separate table for each measure? > Passing --meas flag multiple items did not work. > > Thanks for your help! > Hamdi > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] aparcstats2table -- extracting multiple measures
Dear experts, I am using aparcstats2table to extract values on a number of measures like thickness, curvature, folding index, and surface area for specific ROIs. Is it possible to create a table (using aparcstats2table) with all these measures included or do I have to run it separately and create a separate table for each measure? Passing --meas flag multiple items did not work. Thanks for your help! Hamdi ___ 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 - comparing two groups within a ROI
Hi Doug,
Thanks for the reply. Sure I will try this command. But as it is now, how will
mri_segstats know the order in the fsgd file? Also, this command needs to run
for each subject, right? Then, which input file should I use for the --i flag?
mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh--id 1
--avgwf y.label.dat
Thanks a lot!
Hamdi
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: Tuesday, November 03, 2015 2:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical thickness - comparing two groups within a ROI
On 10/30/2015 01:36 PM, Eryilmaz, H. Hamdi wrote:
> Sorry, the figures I inserted in the text did not appear in the email.
> I attach them now.
>
> Best,
> Hamdi
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eryilmaz, H.
> Hamdi [hamdi.eryil...@mgh.harvard.edu]
> *Sent:* Friday, October 30, 2015 1:32 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] cortical thickness - comparing two groups
> within a ROI
>
> Dear FS experts,
>
> I have a question about extracting average cortical thickness from a
> manually created ROI. I am comparing 2 groups, namely PostFort and
> PreFort and my fsgd file appears as the following:
>
> GroupDescriptorFile 1
> Title PostPreFortification
> Class PostFort
> Class PreFort
>
> InputSubject1PostFort
> InputSubject2PostFort
> .
> .
> .
>
> The contrast that I use to compare these groups is [1 -1]. When I
> display the significance map for this contrast I get the following
> image on the left hemisphere:
>
>
>
>
> My first question is, those blue clusters represent regions, where
> thickness is greater in the PreFort group, don't they?
Correct
> Assuming this is correct, I created a label for this region (which
> contains about 3000 vertices) and extracted the thickness value from
> this region for each subject using the following commands. These
> commands are part of scripts in which $subject and $label are defined.
>
>
>
> _to make a label for each subject (the original label was created on
> fsaverage):_
> *mri_label2label* --srclabel $SUBJECTS_DIR/labels/${label}.label
> --srcsubject fsaverage --trglabel
> $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject
> --regmethod surface --hemi lh
>
> _to create a stats file of this ROI containing several anatomical
> measures:_
> *mris_anatomical_stats* -f
> $SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l
> $SUBJECTS_DIR/$subject/label/NP_PostMINUSPre_IPS.label $subject lh
>
> _to compile thickness values from all subjects into one table: _
> *aparcstats2table* --hemi lh --subjectsfile
> $SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --parc
> NP_PostMINUSPre_IPS.label --meas thickness --tablefile
> $SUBJECTS_DIR/Analyses_Thickness/Tables/LH_NP_PostMINUSPre_IPS_stats.txt
>
> This table displays the average thickness value of my ROI for each
> subject. Based on this table I calculated the mean thickness for each
> group, which is as the following:
>
> PostFort: 3.043
> PreFort: 2.842
>
> My question is: If this cluster appears blue in the Post>Pre map,
> shouldn't the thickness have been greater in the PreFort group? Or am
> I missing a step?
Not sure. The commands look right. Can you try something else?
mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh
--id 1 --avgwf y.label.dat
This should create a single column of numbers in y.label.dat that
correspond to the mean thickness in the label of each subject as
ordered in your fsgd file. See if you get similar numbers to your method
doug
>
> Many thanks in advance!
>
> Best,
> Hamdi
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Re: [Freesurfer] cortical thickness - comparing two groups within a ROI
Hi Doug,
I used the following command for mris_preproc to concatenate the maps from 214
subjects:
mris_preproc --f /$SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --target
fsaverage --hemi lh --meas thickness --out
/$SUBJECTS_DIR/Analyses_Thickness/214_PrePostFort/LH/lh_thickness_map.mgh
Does the order in the subject list file I specified in the --f flag above need
to be exactly the same as in the fsgd files I later used (below) to compare the
groups? If so, that might be the source of the problem. Here's my mri_glmfit
command:
mri_glmfit --y
/$SUBJECTS_DIR/Analyses_Thickness/214_PrePostFort/LH/lh_thickness_map.mgh
--fsgd /$SUBJECTS_DIR/fsgd/RPDR_083115/102PostFort_Minus_112PreFort.fsgd --C
/$SUBJECTS_DIR/fsgd/Top_Minus_Bottom.mtx --glmdir
/cluster/deplin/chris/data/Subjects/Analyses_Thickness/214_PrePostFort/LH/lh_thickness_fwhm22
--surf fsaverage lh --fwhm 22 --no-prune
Thanks!
Hamdi
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: Tuesday, November 03, 2015 2:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical thickness - comparing two groups within a ROI
The y.mgh file is created by your call to mris_preproc (or by a
subsequent call to mri_surf2surf for smoothing). The order of the
subjects depends on how you called mris_preproc (which should match that
in the fsgd file or else everything will be bogus). The y.mgh file
contains all the subjects in fsaverage space, so you don't need to run
it for each subject or resample back into native space
On 11/03/2015 02:29 PM, Eryilmaz, H. Hamdi wrote:
> Hi Doug,
>
> Thanks for the reply. Sure I will try this command. But as it is now, how
> will mri_segstats know the order in the fsgd file? Also, this command needs
> to run for each subject, right? Then, which input file should I use for the
> --i flag?
>
> mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh--id 1
> --avgwf y.label.dat
>
>
> Thanks a lot!
> Hamdi
>
>
> 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: Tuesday, November 03, 2015 2:01 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] cortical thickness - comparing two groups within a
> ROI
>
> On 10/30/2015 01:36 PM, Eryilmaz, H. Hamdi wrote:
>> Sorry, the figures I inserted in the text did not appear in the email.
>> I attach them now.
>>
>> Best,
>> Hamdi
>>
>> ----
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eryilmaz, H.
>> Hamdi [hamdi.eryil...@mgh.harvard.edu]
>> *Sent:* Friday, October 30, 2015 1:32 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* [Freesurfer] cortical thickness - comparing two groups
>> within a ROI
>>
>> Dear FS experts,
>>
>> I have a question about extracting average cortical thickness from a
>> manually created ROI. I am comparing 2 groups, namely PostFort and
>> PreFort and my fsgd file appears as the following:
>>
>> GroupDescriptorFile 1
>> Title PostPreFortification
>> Class PostFort
>> Class PreFort
>>
>> InputSubject1PostFort
>> InputSubject2PostFort
>> .
>> .
>> .
>>
>> The contrast that I use to compare these groups is [1 -1]. When I
>> display the significance map for this contrast I get the following
>> image on the left hemisphere:
>>
>>
>>
>>
>> My first question is, those blue clusters represent regions, where
>> thickness is greater in the PreFort group, don't they?
> Correct
>> Assuming this is correct, I created a label for this region (which
>> contains about 3000 vertices) and extracted the thickness value from
>> this region for each subject using the following commands. These
>> commands are part of scripts in which $subject and $label are defined.
>>
>>
>>
>> _to make a label for each subject (the original label was created on
>> fsaverage):_
>> *mri_label2label* --srclabel $SUBJECTS_DIR/labels/${label}.label
>> --srcsubject fsaverage --trglabel
>> $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject
>> --regmethod surface --hemi lh
>>
>> _to create a stats file of this ROI containing several anatomical
>> measures:_
>> *mris_anatomical_stats* -f
>> $SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l
>> $SUBJE
[Freesurfer] cortical thickness - comparing two groups within a ROI
Dear FS experts,
I have a question about extracting average cortical thickness from a manually
created ROI. I am comparing 2 groups, namely PostFort and PreFort and my fsgd
file appears as the following:
GroupDescriptorFile 1
Title PostPreFortification
Class PostFort
Class PreFort
InputSubject1PostFort
InputSubject2PostFort
.
.
.
The contrast that I use to compare these groups is [1 -1]. When I display the
significance map for this contrast I get the following image on the left
hemisphere:
[X]
My first question is, those blue clusters represent regions, where thickness is
greater in the PreFort group, don't they? Assuming this is correct, I created a
label for this region (which contains about 3000 vertices) and extracted the
thickness value from this region for each subject using the following commands.
These commands are part of scripts in which $subject and $label are defined.
[X]
to make a label for each subject (the original label was created on fsaverage):
mri_label2label --srclabel $SUBJECTS_DIR/labels/${label}.label --srcsubject
fsaverage --trglabel $SUBJECTS_DIR/$subject/label/$label.label --trgsubject
$subject --regmethod surface --hemi lh
to create a stats file of this ROI containing several anatomical measures:
mris_anatomical_stats -f
$SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l
$SUBJECTS_DIR/$subject/label/NP_PostMINUSPre_IPS.label $subject lh
to compile thickness values from all subjects into one table:
aparcstats2table --hemi lh --subjectsfile
$SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --parc
NP_PostMINUSPre_IPS.label --meas thickness --tablefile
$SUBJECTS_DIR/Analyses_Thickness/Tables/LH_NP_PostMINUSPre_IPS_stats.txt
This table displays the average thickness value of my ROI for each subject.
Based on this table I calculated the mean thickness for each group, which is as
the following:
PostFort: 3.043
PreFort: 2.842
My question is: If this cluster appears blue in the Post>Pre map, shouldn't the
thickness have been greater in the PreFort group? Or am I missing a step?
Many thanks in advance!
Best,
Hamdi
___
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] selxavg3-sess error
Dear FS experts, I got an error while running selxavg3-sess for a single subject. The log (attached) says the following: * ** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions! Input: nx=64 ny=64 nz=35 Base: nx=64 ny=64 nz=37 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg * I am wondering which 'template.nii' file the script reads to create tempvol.nii.gz. We have different functional runs (with different TRs) under the subject's bold directory and for the run '/018' the TR should be 1900 ms. It looks like the script is reading from a 'template.nii' located elsewhere for which the TR is 2000 ms. * reading from template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998769, -0.00721698, 0.0490727) j_ras = (-1.73634e-08, -0.989358, -0.145502) k_ras = (0.0496006, -0.145323, 0.98814) changing data type from short to float (noscale = 0)... writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz... * Many thanks for your help! Hamdi -- Hamdi Eryilmaz, PhD Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462 Email: hamdi.eryil...@mgh.harvard.edumailto:heryil...@partners.org selxavg3-sess log file /usr/local/freesurfer/stable5_0_0/fsfast/bin/selxavg3-sess -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/FruitTask_030815 -analysis FT_TEST -overwrite $Id: selxavg3-sess,v 1.52.2.5 2010/08/25 19:07:37 greve Exp $ uid=3429288(hhe0) gid=3429288(hhe0) groups=3429288(hhe0),1506(roffmagp) /autofs/cluster/roffman/users/Stable5_PerRun Linux audrey 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Sun Mar 8 18:17:22 EDT 2015 preproc-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -a FT_TEST -nolog -- preproc-sess logfile is /dev/null -- $Id: preproc-sess,v 1.31.2.6 2011/01/10 17:05:53 greve Exp $ hhe0 setenv FREESURFER_HOME /usr/local/freesurfer/stable5_0_0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun Linux audrey 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_0_0/fsfast/bin/preproc-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -a FT_TEST -nolog Sun Mar 8 18:17:22 EDT 2015 instem f mc 1 f fmc stc 0 fmc sm 1 fmc fmc.sm5 mask 1 brain GDDA074 Template - mktemplate-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistFT -nolog -update Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA074 Sun Mar 8 18:17:22 EDT 2015 Detected input format at nii GDDA074 Update not needed Run: 018 Sun Mar 8 18:17:22 EDT 2015 GDDA074 018 Update not needed Sun Mar 8 18:17:22 EDT 2015 mktemplate-sess completed GDDA074 Mask mkbrainmask-sess -maskstem brain -fsd bold -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistFT -nolog -update /autofs/cluster/roffman/users/Stable5_PerRun/GDDA074 Sun Mar 8 18:17:22 EDT 2015 GDDA074 Update not needed for session-level mask GDDA074 Update not needed for run 018 mask GDDA074 Update not needed for run 018 meanval Sun Mar 8 18:17:22 EDT 2015 mkbrainmask-sess done GDDA074 Registration - register-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistFT -per-session -nolog -update -- register-sess logfile is /dev/null -- Sun Mar 8 18:17:23 EDT 2015 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_0_0/fsfast/bin/register-sess -s GDDA074 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistFT -per-session -nolog -update freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319 Linux audrey 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA074 Sun Mar 8 18:17:23 EDT 2015 /autofs/cluster/roffman/users/Stable5_PerRun/GDDA074 Sun Mar 8 18:17:23 EDT 2015 register-sess completed GDDA074 MC - mc-sess -fstem f -fmcstem fmc -s GDDA074 -d
Re: [Freesurfer] selxavg3-sess error
Hi Doug, Yes, that's correct. Images in runs 015,016,017 have 37 slices, those in run 018 have 35. Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, March 09, 2015 2:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error It looks like different runs have different number of slices. Is that right? On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote: Dear FS experts, I got an error while running selxavg3-sess for a single subject. The log (attached) says the following: * ** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions! Input: nx=64 ny=64 nz=35 Base: nx=64 ny=64 nz=37 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg * I am wondering which 'template.nii' file the script reads to create tempvol.nii.gz. We have different functional runs (with different TRs) under the subject's bold directory and for the run '/018' the TR should be 1900 ms. It looks like the script is reading from a 'template.nii' located elsewhere for which the TR is 2000 ms. * reading from template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998769, -0.00721698, 0.0490727) j_ras = (-1.73634e-08, -0.989358, -0.145502) k_ras = (0.0496006, -0.145323, 0.98814) changing data type from short to float (noscale = 0)... writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz... * Many thanks for your help! Hamdi -- Hamdi Eryilmaz, PhD Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462 Email: hamdi.eryil...@mgh.harvard.edumailto:heryil...@partners.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] selxavg3-sess error
We use 'preproc-sess' before a single subject analysis. Here are the commands we run: preproc-sess -s SUBJECT_ID -fwhm 5 -per-run mkanalysis-sess -analysis FT_TEST -TR 1.9 -paradigm FT.par -event-related -runlistfile runlistFT -native -fwhm 5 -mcextreg -nconditions 10 -gammafit 2.25 1.25 -refeventdur 2 -force 'preproc-sess' is run for all runs by default. Do you think we should run a separate 'preproc-sess' for each run? Thanks! Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, March 09, 2015 2:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error What is your mris_preproc command? And your mkanalysis-sess command? On 3/9/15 2:41 PM, Eryilmaz, H. Hamdi wrote: Hi Doug, Yes, that's correct. Images in runs 015,016,017 have 37 slices, those in run 018 have 35. Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, March 09, 2015 2:38 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error It looks like different runs have different number of slices. Is that right? On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote: Dear FS experts, I got an error while running selxavg3-sess for a single subject. The log (attached) says the following: * ** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions! Input: nx=64 ny=64 nz=35 Base: nx=64 ny=64 nz=37 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg * I am wondering which 'template.nii' file the script reads to create tempvol.nii.gz. We have different functional runs (with different TRs) under the subject's bold directory and for the run '/018' the TR should be 1900 ms. It looks like the script is reading from a 'template.nii' located elsewhere for which the TR is 2000 ms. * reading from template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998769, -0.00721698, 0.0490727) j_ras = (-1.73634e-08, -0.989358, -0.145502) k_ras = (0.0496006, -0.145323, 0.98814) changing data type from short to float (noscale = 0)... writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz... * Many thanks for your help! Hamdi -- Hamdi Eryilmaz, PhD Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462 Email: hamdi.eryil...@mgh.harvard.edumailto:heryil...@partners.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
