Freesurfer July 2021

freesurfer@nmr.mgh.harvard.edu

91 participants
121 discussions

niiRead: error opening file, through mri_convert
by Andrew 02 Aug '21

02 Aug '21

External Email - Use Caution Hello, I’m trying to reconstruct an old pipeline that I don’t completely understand (so sorry if this is very elementary or out of date), and one step is to convert the freesurfer T1 segmentation ribbon.mgz to .nii format using mri_convert. Through freesurfer interface I see the T1 and the segmentation are fine; but mri_convert seems to fail on looking for the T1: The command (from inside Matlab) is: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii Output looks like: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) reading template info from volume /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii... error: niiRead(): error opening file /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii***** It is failing to read the T1 and then it does not save the output file. But the input files (T1.nii and ribbon.mgz) are all where they should be. What could I be doing wrong? thanks, -Andrew

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SAMstats2table option
by AJ 02 Aug '21

02 Aug '21

External Email - Use Caution Hi, I was wondering if there is a simple command for generating a table from all the SamsegOutput/stats files across all subjects. When I use the asegstats2table, I get index error: list index out of range. I guess this has to do with the structure of files in the samsegOutput/stats versus the aseg.stats file? Thank you. AJ

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vol2subfield: which file to use?
by Shane Schofield 02 Aug '21

02 Aug '21

External Email - Use Caution Hi Freesurfer Tema, I am trying to use vol2subfield to extract DTI measurements like FA and MD. For this purpose, should I be using the rh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz or rh.hippoAmygLabels-T1.v21.CA.mgz ? Thank you!

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Problem with images captured through quicksnaps.tiff in Qdec
by Koustav Chatterjee 02 Aug '21

02 Aug '21

External Email - Use Caution Dear Forum members, In 'qdec' I was trying to use quicksnaps.tiff and as a result of which 4 images (different view) automatically saved into specific destinations. However, the images are completely black, nothing can be visible. Can you please tell what I did wrong? [image: image.png] Thank you for your time and help. Regards, KC

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Re: [Freesurfer] (no subject)
by Stephanie K 02 Aug '21

02 Aug '21

External Email - Use Caution Hello, Can you please clarify the following: Do we use subcortical QC rating for all subcortical measures such as accumbens as well measures such as total white matter volume. We do not use it for estimated total intracranial volume as this is accurately measured? Do we use cortical QC rating for all regional cortical measures but not the global measures (e.g. mean thickness/total surface area) as these are accurately parcellated? Sorry for my very basic questions. I am using already processed data and only using the statistics for brain MRI data Thanks, Stephanie

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Error with running retinotopy glm
by Yaoda Xu 02 Aug '21

02 Aug '21

Dear all, Using FreeSurfer 7.1.1, I made my analysis file with the following (I assume -nksip should be in the number of TRs and not in seconds): mkanalysis-sess -analysis retino_surf_pr_lh_sm0 -surface self lh -fwhm 0 -fsd bold -per-run -retinotopy 32 -spmhrf 0 -paradigm retino.par -TR .800 -nskip 10 -mcextreg -runlistfile retino_all_runs.txt Then I ran the glm with the following: selxavg3-sess -sf sessid_retino -df sessdir -analysis retino_surf_pr_lh_sm0 But I kept getting the following error message at the end of the log file: -------------------------fast_selxavg3b.m 7.1.1———————————— outtop = /gpfs/milgram/scratch60/chun/yx55/mri-space/studies/localizers/unpackdata Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 12, skipping Excluding 10 points nruns = 4 autostimdur = outanadir = /gpfs/milgram/scratch60/chun/yx55/mri-space/studies/localizers/unpackdata/20210719_localizer_10/bold/retino_surf_pr_lh_sm0 Excluding 10 points Excluding 10 points Excluding 10 points Excluding 10 points Found 125600/133962 (93.8) voxels in mask 1 Creating Design Matrix ... creation time = 0.007 sec DoMCFit = 1 ntptot = 1380, nX = 88, DOF = 1292 Saving X matrix to /gpfs/milgram/scratch60/chun/yx55/mri-space/studies/localizers/unpackdata/20210719_localizer_10/bold/retino_surf_pr_lh_sm0/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3b (line 389) XCond = cond(XtX); >> ————————————————————— ERROR: fast_selxavg3() failed\n How should I fix this error? Any suggestions would be greatly appreciated. Thanks so much! Best, Yaoda Xu External Email - Use Caution

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Intensity equalization
by AJ 02 Aug '21

02 Aug '21

External Email - Use Caution Hi, I have 2 MRIs on different scanners. The tissue contrasts are slightly off and there is slight differences in the volumes of ROIs. Is there a way to make both MRIs have the same intensity? I.e., Im2's intensity follows Im1's intensity? Many thanks AJ

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selective pial edits
by Kishore Vakamudi 02 Aug '21

02 Aug '21

External Email - Use Caution Dear Freesurfer Experts, Is there any way to remove pial edits selectively after you go through the first round of edits and save the brain mask? Details: I've pial edited for a few brains and saved their brain masks. But when I was going through a second time, I realized some of the edits are not necessary or need an edit. I know -clean-bm will remove all edits. But is there any way to edit selectively after first round of edits and before running the second recon-all? Thank you in advance, Kishore -- *Kishore Vakamudi * Research Analyst II The Mind Research Network | 1101 Yale Blvd NE, Albuquerque, NM 87106

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Total WM surface area
by Alexopoulos, Dimitrios 02 Aug '21

02 Aug '21

External Email - Use Caution Hi, Are the total lh/rh cortical surface areas in stats/aparc.stats = parcel1 surface area + parcel2 surface area…? Get Outlook for Android<https://secure-web.cisco.com/1r8EgoSfTlXwlAPQCeMBRYJ0_aOaAble6354Xo7obkuwMZ…> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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SAMSEG seg output contains holes
by Simon Jones 02 Aug '21

02 Aug '21

External Email - Use Caution Dear all I have tried using SAMSEG in 7.1.1 with 7T MP2RAGE sequence data which has an inv1, inv2 and a uni images and I can create a denoised image which has a more of a traditional T1-weighted appearance. I have got some good looking results combining the uni with the inv2 except for one issue. About 20% have a small hole or slit produced within the frontal lobe. It is like an echo of the frontal sinuses and seems to appear whichever image is input. For others, the hole is outside the brain. Is this just a feature? Thanks for your help Simon

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Freesurfer July 2021