Freesurfer July 2016

freesurfer@nmr.mgh.harvard.edu

143 participants
252 discussions

Error with local Gyrification Index (lGI)
by Mahtab Farahbakhsh 07 Jul '16

07 Jul '16

Dear FreeSurfer, I am trying to calculate LGI for my images, but it seems like that it doesn't work. I have tried everything, but it's still giving me the same error. I'm using FreeSurfer on a mac and my Matlab version is R2016a. When I try to run "recon-all -s <subj> -localGI", I get this error: ERROR: Matlab is required to run mris_compute_lgi!. I have done these so far: PATH=/Applications/MATLAB_R2016a.app/bin/matlab:$PATH export PATH And my $PATH is: /Applications/MATLAB_R2016a.app/bin/matlab:/usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/opt/X11/bin: No such file or directory And when I write getmatlab, I get this: ERROR: Cannot find matlab. Does not exist or is not in path. My original Matlab is in the /Applications folder and I also have a folder named "matlab" in my FreeSurfer folder. Would you please guide me what I should do? Best Regards, Mahtab.

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Recon-all error after El Capitain update
by stdp82＠virgilio.it 07 Jul '16

07 Jul '16

Hi list, after update with El Capitain, recon-all -all produce the error reported below. Thanks srclabel = /Applications/freesurfer/subjects/subject_prova/subj/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = SUBJECTS_DIR trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova/subj FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory ERROR reading /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh.BA1.label Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0: root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s SUBJECTS_DIR exited with ERRORS

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mris_preproc subject-volume mismatch
by Raney, Talia L. 07 Jul '16

07 Jul '16

Hi FreeSurfer users, I'm trying to use mri-preproc to do a group fMRI analysis(based on the tutorial). However, I keep getting an error that the number of input volumes does not equal number of subjects. It seems one volume is counted as 4 subjects. I'm wondering what the command determines to be the subject list when you use the --iv flag. For reference, I'm basing it off of this command: mris_preproc --target fsaverage --hemi lh \ --iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ --iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ --iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ --iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ --iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ --projfrac 0.5 \ --out lh.ces.mgh Thanks! Talia

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recon-all exited with error: reading lh.BA1_exvivo.label
by Vaz pandolfo, Renata 07 Jul '16

07 Jul '16

Dear FreeSurfer developers, I am running recon-all on a healthy subject and I am also trying to get the hippocampal subfields segmentation. On the mri directory there is no hippocampus output, and the recon-all exited with errors. >From my understanding, the error is with the lh.BA1_exvivo.label: SUBJECTS_DIR /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815 FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label The command I used was: recon-all -all \ -i ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz -s 20110815/ \ -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ -T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \ -T2pial -hippocampal-subfields-T1 When trying to solve the problem, I noticed that I could have run a separate command for the hippocampal subfields and I ran this one: recon-all \ -s 20110815/ \ -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ -hippocampal-subfields-T1T2 ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz 20110815_T2 Since the previous data had errors, I didn't really expect this to work, but I tried it anyways. It exited "without errors", but on the log there was the following error twice: Error:Cannot find CTF archive /usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf Extra info: Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611 uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux logs: recon-all and hippocampal-subfields-T1T2 attached If anyone has had the same problem, could you please tell me how to solve it? And if I am doing something wrong, please tell me the correct way so I can continue with the analysis. Thank you! Renata

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Freeview: how to change spline color bar
by Barbara Kreilkamp 07 Jul '16

07 Jul '16

Dear Freesurfers, How would I be able to use a different colormap under point sets please? I can only find "solid color" and "heatmap" but a blue to red colorbar would suit my needs more. Any assistance is greatly appreciated. Thank you, Best wishes, Barbara

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Qdec-correction for multiple comparison
by John Anderson 06 Jul '16

06 Jul '16

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Seed based volume output to surface
by Taha Abdullah 06 Jul '16

06 Jul '16

Good Afternoon Freesurfers, I am running a seed-based connectivity for one individual subject. The seed is in the L_parahippocampus. I have followed the steps outlined in FSFast walkthrough. Below is a list of my commands. Mind you that I was trying to keep my analysis as simple as possible before delving deeper into it. I have a question on the sig.nii.gz output. Please see at the end. preproc-sess -s taha_brain -fwhm 0 -surface self lhrh -mni305-2mm -fsd resting_scans -per-run fcseed-config -segid 1016 -fcname L_parahipp -fsd resting_scans -mean -cfg mean.L_parahipp.config -overwrite -fillthresh 1 fcseed-sess -s taha_brain -cfg mean.L_parahipp.config mkanalysis-sess -analysis L_parahipp_seed.surf.lh -surface self lh -fwhm 0 -notask -taskreg L_parahipp 1 -fsd resting_scans -TR 0.555 -mcextreg -polyfit 2 -per-run selxavg3-sess -s taha_brain -a L_parahipp_seed.surf.lh Output files /home/tabdullah/Project/Sess01/fsd/L_parahipp_seed.surf.lh/L_parahipp/sig.nii.gz amongst others *Is there a way to convert the volume to a surface and then extract per vertex the sig value?* I used tmri_vol2surf see below: mri_vol2surf --mov ./sig.nii.gz --reg /home/tabdullah/resting_state_1/taha_brain/resting_scans/001/register.dof6.dat --trgsubject taha_brain --interp nearest --projfrac 0.5 --hemi lh --o /home/tabdullah/sig.mgh --noreshape --cortex I tried using mris_convert -c mris_convert -c ./sig.mgh /usr/local/freesurfer/subjects/taha_brain/surf/lh.white sig.asc The last column is all zeros. I am not entirely sure what I am doing wrong here, it is probably somewhere in the last two commands. Possibly using mri_segstats or mri_read.m? Any help would be greatly appreciated. Apologize in advance for the long email. -- Taha Abdullah Department of Physiology Northwestern University Feinberg School of Medicine Masters of Science Physiology and Biophysics, Georgetown University 2015 Work: (312)-503-0413

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Design Matrix Creation
by Timothy Hendrickson 06 Jul '16

06 Jul '16

Freesurfer Support, Thank you for your support with my previous line of questions regarding design matrix creation. I have manually created another design matrix and want to ensure that I designed it correctly. An example of my FSGD file is as follows below: Class SITE 1-Male-Control Class SITE 1-Male-PATIENT Class SITE 1-Female-Control Class SITE 1-Female-PATIENT Class SITE 2-Male-Control Class SITE 2-Male-PATIENT Class SITE 2-Female-Control Class SITE 2-Female-PATIENT Class SITE 3-Male-Control Class SITE 3-Male-PATIENT Class SITE 3-Female-Control Class SITE 3-Female-PATIENT Class SITE 4-Male-Control Class SITE 4-Male-PATIENT Class SITE 4-Female-Control Class SITE 4-Female-PATIENT Variables age_at_scan total_intracranial_volume study site levels = 1, 2, 3, 4 gender levels = Male, Female diagnosis levels = PATIENT, Control age_at_scan = covariate age total_intracranial_volume = covariate total intracranial volume What I would ideally like to do is: 1) Take into account offset differences amongst diagnosis, gender, and study site. 2) Allowing a difference in age slope, and total intracranial volume slope amongst the diagnosis and gender levels. 3) Modeling the age slope and total intracranial volume slope as the same for the study site levels. Let's image that the first participant is from site 1, Male, and control, and is 12 and has a TIV of 30,000. The second participant is from site 2, Female, and PATIENT, and is 14, and has a TIV of 25,000. My understanding of the design matrix would be as follows: 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 30000 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 25000 -Tim >Yes, create your matrix manually. > >Those matrix lines are not quite right. The ages are in the correct >column, but you need a 1 somewhere in columns 1-8 to indicate the class >(ie, site/dx) that the subject is in. On 05/26/2016 12:57 PM, Timothy Hendrickson wrote: > Hi Doug, > > Thank you for such a prompt response. Just to be clear you are > recommending that I manually create the matrix file right? > > If so I want to ensure that I am understanding how to design the > matrix file properly. > > Let's imagine that the first participant is a control and is 13 and > the second is a patient and is 15. My understanding is that the matrix > file would be as follows: > 0 0 0 0 0 0 0 0 13 0 > 0 0 0 0 0 0 0 0 0 15. > > -Tim > Previous correspondences are below: > > You'll need a regressor for each of the 8 classes you describe below. > You can use mri_glmfit to generate this (Xg.dat file) > You'll need two more regressors for age, one for each diagnosis. If a > subject (ie, row) is a control then the two values will be AGE 0. If the > subject of the row is a patient, then the two values will be 0 AGE. You > can then set up a Controls-Patients age (ie, interaction between dx and > age) contrast like > [0 0 0 0 0 0 0 0 1 -1] > On 05/24/2016 02:30 PM, Timothy Hendrickson wrote: > > > > Freesurfer Support, > > > > I'd like to create a design matrix for a group analysis outside of the > > DODS and DOSS models. I understand that in order to do this the -X > > flag must be used. However, I have been unable to find examples of how > > to do this. > > > > I am hoping to reveal a difference in thickness or gyrification > > amongst a clinical population. The data set contains two factors: > > diagnosis, and study site and one covariate: age. Diagnosis has two > > levels: controls, and patients. Study site has four levels, one level > > for each location the data has been collected from. > > > > What I would ideally like to do is: > > > > 1) Take into account offset differences amongst diagnosis and study site. > > > > 2) Allowing a difference in age slope amongst the diagnosis levels > > > > 3) Modeling the age slope as the same for the study site levels > > > > My FSGD file is designed as follows > > > > Class SITE 1-Control > > Class SITE 1-PATIENT > > Class SITE 2-Control > > Class SITE 2-PATIENT > > Class SITE 3-Control > > Class SITE 3-PATIENT > > Class SITE 4-Control > > Class SITE 4-PATIENT > > Variables age_at_scan > > > > study site levels = 1,2,3 and 4 > > diagnosis levels = PATIENT and Control > > age_at_scan = covariate age > > > > Any advice would be greatly appreciated. > > > > Respectfully, > > > > Tim > > > > -- > > Timothy Hendrickson > > Department of Psychiatry > > University of Minnesota > > Mobile: 507-259-3434 <tel:507-259-3434> (texts okay)

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FSFAST- Cerebellum
by Sabin Khadka 06 Jul '16

06 Jul '16

Hi all, I am trying to extract mean time series BOLD data using FSFAST from Cortical ROIs + sub cortical ROIs and cerebellum. preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd mri_segstats --annot fsaverage lh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt mri_segstats --annot fsaverage rh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt and for cortical time series mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf subCorticalTimeSeries.txt But I am not sure on how exactly to extract time series from cerebellar regions. So if I want to extract time series from regions as described in Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in FreeSurferCololLUT.txt? If not could you please direct me to processes that I can use. Cheers, Sabin Khadka

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Intensity stats question
by Sabrina Yu 06 Jul '16

06 Jul '16

Hello, I have a couple of questions about the wmparc.stats file generated. What volume is the data based on? Has the intensity of the volume been corrected? I just need the average voxel intensity over the ROIs, but am unsure if this intensity is based on an intensity normalized brain volume. Is it possible to change the input volume for wmparc.stats to orig.mgz? Thank you in advance.

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Freesurfer July 2016