Freesurfer

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30097 discussions

make_average_template error
by Chatzi, Vasiliki 07 Jul '16

07 Jul '16

* Hello freesurfer developers, I am trying to compute the average_subject template described in the freesurfer wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject) I have located all the subjects' directories in one folder named All_data_baseline. Then I set SUBJECTS_DIR to this folder using the command setevn SUBJECTS_DIR ./ ,and then I defined the subjects using the command setenv SUBJECTS = (subject1 subject2 ...). Finally I run the command make_average_subject --out avgsubject. The directory avgsubject was created but then I received the following error: error.log: MRISread (.//subject1/surf/lh.sphere.reg): could not open file mris_make_template: could not read surface file .//subject1/surf/lh.sphere.reg error as it appears on the terminal: output subject: avgsubject mri_add_xform_to_header -c auto .//avgsubject/mri/mni305.cor.mgz .//avgsubject/mri/mni305.cor.mgz INFO: extension is mgz tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory #@# Making lh registration template --------- tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory /homedirectory/All_data_baseline/avgsubject tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory mris_make_template -norot -annot aparc lh sphere.reg subject1 tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization... processing subject subject1 (1 of 313) reading spherical surface .//subject1/surf/lh.sphere.reg... MRISread(.//subject1/surf/lh.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file .//subject1/surf/lh.sphere.reg No such file or directory ERROR: make_average_surface I did search the make_average_subject --help and the mail archive but I have not yet found a solution. Please accept my apologies if there is one but I have not noticed. I am using version freesurfer-5.3.0 in a Linux 7.1 with 48 core memory. I was wondering if you could possibly provide any advice for troubleshooting this error. Best wishes, Vasiliki

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LGI Summary Statistics
by Timothy Hendrickson 07 Jul '16

07 Jul '16

Freesurfer Support, I have seen previous message threads on extracting LGI measurements across ROIs, however I have yet to find anything which would provide a summary LGI across an entire hemsphere. Other measurements like cortical thickness have a measurement like this. Is there a measurement like this for LGI? If I take the mean of all of the ROIs would that be equivalent to a hemispheric LGI measure? Thanks! -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

2 1

FOV Size Discrepancy
by Tamara Tavares 07 Jul '16

07 Jul '16

Hello! I was hoping someone can provide me with some clarification on an issue I have been having with the FOV size. I have a database of scans which I am running through recon-all cross-sectionally. The majority of the scans have an FOV of 256x256x208; however, when I run them through recon-all I get an error message indicating that the FOV is larger than 256 (282x282x228). When I use the -cw256 flag, recon-all runs through successfully. I do not understand why recon-all thinks the FOV is larger then it is. I double checked that the FOV size is 256 using the mri_info command line and the database information. Does anyone know why recon-all is listing a larger FOV size? Thank you in advance for your help. Tamara

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question about exporting volumes
by Dorsa Haji Ghaffari 07 Jul '16

07 Jul '16

Hi, I was able to segment the MRI successfully, now I am trying to isolate the thalamus and export it out of FS as a volume. Is there a way to do that in FS? Thank you Dorsa

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Question about Thalamus segmentation
by Dorsa Haji Ghaffari 07 Jul '16

07 Jul '16

Hi, I am trying to segment the thalamus into its nuclei such as VLA , VLP and VIM. I see those labels available in the atlas but I do not get any of them in my segmentation. Does anyone have any idea how to do that? Thank you Dorsa

2 1

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

2 1

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

2 6

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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