Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

Problem flipping a label into other hemisphere
by Neuro Lists 27 Dec '17

27 Dec '17

Hi all, I've searched the lists extensively and have not been able to resolve my problem. I'd greatly appreciated any help. I have run the recon-all pipeline on a number of subjects, made the appropriate fixes and am happy with the surfaces. For each subject, I have a number of ROIs that are created programmatically and they are exactly as they should be. These ROIs are on the "regular" surfaces, not the inflated ones. In other words, opening the brainmask.mgz in freeview and just loading the label file results in the ROI being where I expect it to be. I'm now trying to flip the ROI onto the contralateral hemisphere and this is going terribly wrong. No matter what I try, the ROI ends up being generated far outside of the brain. I was originally trying to use the xhemi pipeline, but then I realized from the forums that I could just use mris_left_right_register. I've done: cd subject/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right I've then tried using a number of varieties of mri_apply_reg that have been listed on the forum: 1) mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere lh.sphere.left_right 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right rh.sphere.left_right --trg rh.lh.source.label No matter what I try though, the flipped ROI ends up being way outside of the brain when I overlay it on the brainmask. Is this because the flipped ROI should instead be visualized on the inflated hemisphere? If so, how can I get it to overlay properly onto the brainmask so that I can be sure it's correct? My ultimate goal is to get anatomical stats from the original and flipped ROIs. Thanks for your help! Joe

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CORRECTING DEFECT recon-all giant cyst
by Loeffler, Martin 27 Dec '17

27 Dec '17

Dear FreeSurfer team, For a case report I'm running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message): CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849) XL defect detected... It is stuck here since a whole day now, so I'm not expecting it to advance... Following this post: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I looked at the wm.mgz, but did not find huge errors. Do you have any ideas what the problem might be or what I can do to work around it? Thanks, Martin

3 7

Problems with surfaces along midline
by Romella Durrani 25 Dec '17

25 Dec '17

Hi, I'm having problems with the surfaces along the midline for one scan. I have attached pictures of the brainmask with surfaces, wm.mgz, and T1 (before any of my edits). I have tried to fix this by adding control points and also tried to fix it by editing the wm.mgz file to fix the ventricle problem, however, none of these edits have resolved the issue. Thanks!

1 0

Thresholding in Tracula
by Duncan Cleveland 25 Dec '17

25 Dec '17

Dear FreeSurfer Group, I have a brief question about how thresholding is conducted in TRACULA. I am looking to threshold path.pd.nii.gz for use as a mask in other analyses. However, I am having difficulty determining the threshold to use to create an appropriate mask. The FreeSurfer literature and wiki suggest that the optimal threshold is 20% of the maximum value. However, this differs from the apparent thresholding used to create the merged_avg file and pathstats.overall.txt. For example, when I load my merged_avg into freeview, the automatic threshold for the forceps major for a given subject is 39.4, and when I threshold path.pd.nii.gz at 39.4, the volume is 679 voxels. This volume matches the volume seen in pathstats.overall.txt. Given that 20% of the maximum is 39.4, I should expect the maximum threshold to have an intensity of 197. However, the maximum threshold is 509, making 39.4 only 7.74% of the maximum value. This suggests that I should threshold path.pd.nii.gz at 101.8. While I used the forceps major as an example, this issue persists across tracts and across subjects. There doesn't appear to be any clear pattern which suggests the tracts are thresholded at a consistent value for all tracts; for one subject, the reported 20% of max is in actuality anywhere from 6.43% to 15.11% of the actual maximum value. I also attempted to force dmri_mergepaths to give me the appropriate maximum value by running the command with a --thresh value of 1. However, the output still opened in freeview with a reported maximum intensity of 197. I am using tracula in FreeSurfer 6.0. How does TRACULA conduct its thresholding within dmri_mergepaths and dmri_pathstats? Why does there appear to be a discrepancy between the reported maximum value and the actual maximum value? And what threshold should I use to create my mask for use outside of FreeSurfer? Thank you for your help. Best, Duncan Cleveland University of Minnesota

2 1

TRACULA question
by Figueiro Longo, Maria Gabriela 25 Dec '17

25 Dec '17

Hi, I am trying to run TRACULA and I am having the same error, after reviewing my directory and the configuration file: "ERROR: run list is longer than subject list" The number of inputs is the same number of subjects. I've read some old emails with similar errors but none of the suggested solutions worked for me. Following a copy of my configuration file. Thanks for the help, Gabriela ------------------------------------------------------------ setenv SUBJECTS_DIR /autofs/cluster/guptagp/gabi/Volume set dtroot = /autofs/cluster/guptagp/gabi/Output set subjlist = (3LT043_s1_170520 3LT043_s2_170715 3LT043_s3_170829 3LT044_s1_170526 3LT044_s2_170607 3LT044_s3_170822 3LT046_s1_170609 3LT046_s2_170620 3LT046_s3_170929 ) set baselist = (3LT043 3LT043 3LT043 3LT044 3LT044 3LT044 3LT046 3LT046 3LT046 ) set dcmlist = ( /autofs/cluster/guptagp/gabi/Diffusion/3LT043_s1_170520.nii.gz /autofs/cluster/guptagp/gabi/Diffusion/3LT043_s2_170715.nii.gz /autofs/cluster/guptagp/gabi/Diffusion/3T043_s3_170829.nii.gz /autofs/cluster/guptagp/gabi/Diffusion/3LT044_s1_170526.nii.gz /autofs/cluster/guptagp/gabi/Diffusion/3LT044_s2_170607.nii.gz /autofs/cluster/guptagp/gabi/Diffusion/3LT044_s3_170822.nii.gz /autofs/cluster/guptagp/gabi/Diffusion/3LT046_s1_17060.nii.gz /autofs/cluster/guptagp/gabi/Diffusion/3LT046_s2_170620.nii.gz /autofs/cluster/guptagp/gabi/Diffusion/3LT046_s3_170929.nii.gz ) set bvallist = (/autofs/cluster/guptagp/gabi/Diffusion/3LT043_s1_170520.bvals /autofs/cluster/guptagp/gabi/Diffusion/3LT043_s2_170715.bvals /autofs/cluster/guptagp/gabi/Diffusion/3LT043_s3_170829.bvals /autofs/cluster/guptagp/gabi/Diffusion/3LT044_s1_170526.bvals /autofs/cluster/guptagp/gabi/Diffusion/3LT044_s2_170607.bvals /autofs/cluster/guptagp/gabi/Diffusion/3LT044_s3_170822.bvals /autofs/cluster/guptagp/gabi/Diffusion/3LT046_s1_17060.bvals /autofs/cluster/guptagp/gabi/Diffusion/3LT046_s2_170620.bvals /autofs/cluster/guptagp/gabi/Diffusion/3LT046_s3_170929.bvals ) set bveclist = ( /autofs/cluster/guptagp/gabi/Diffusion/3LT043_s1_170520.voxel_space.bvecs /autofs/cluster/guptagp/gabi/Diffusion/3LT043_s2_170715.voxel_space.bvecs /autofs/cluster/guptagp/gabi/Diffusion/3LT043_s3_170829.voxel_space.bvecs /autofs/cluster/guptagp/gabi/Diffusion/3LT044_s1_170526.voxel_space.bvecs /autofs/cluster/guptagp/gabi/Diffusion/3LT044_s2_170607.voxel_space.bvecs /autofs/cluster/guptagp/gabi/Diffusion/3LT044_s3_170822.voxel_space.bvecs /autofs/cluster/guptagp/gabi/Diffusion/3LT046_s1_17060.voxel_space.bvecs /autofs/cluster/guptagp/gabi/Diffusion/3LT046_s2_170620.voxel_space.bvecs /autofs/cluster/guptagp/gabi/Diffusion/3LT046_s3_170929.voxel_space.bvecs ) ________________________________

2 1

running longitudinal TRACULA on a subset of already processed baseline DTI scans?
by Fred Sampedro 25 Dec '17

25 Dec '17

Dear TRACULA users, I ran near 100 subjects through the standard (cross-sectional) TRACULA pipeline. Some of them (about 70) have also a longitudinal DTI scan 1-year after the already processed scans. I would like to run longitudinal TRACULA to obtain for those 70 subjects longitudinal changes in FA/MD in the major white matter tracts. My question is: should I specify in the longitudinal dmrirc file that the 80 baseline subjects have already been processed? Will tracula already know it and not re-compute? Could you please provide a fully-working sample dmrirc file for this scenario so I could see the format? I’ve found this pdf https://ftp.nmr.mgh.harvard.edu/pub/docs/TraculaNov2013/tracula.workshop.v.… only but didn’t manage to solve my questions. Thanks a lot in advance, Fred Sampedro, PhD Hospital de Sant Pau (Barcelona)

2 1

Concatenating to run a cortical thickness analysis between 3 groups
by Rosalia Dacosta Aguayo 23 Dec '17

23 Dec '17

Dear FreeSurfer team, I have run recon-all and I have done smoothing in a sample of 24 participants which are divided into 3 groups. Now that I know which smoothing I would like to use, I am a bit lost regarding which of the files generated should I use and how I should concatenate them. It is my first time with FreeSurfer and I would much appreciate your help here. FreeSurfer version is the last release. I am working with Linux mint. Merry Christmas, Rosalia

1 2

Units of GI
by Martin Juneja 22 Dec '17

22 Dec '17

Hi, I came across several papers e.g. http://www.sciencedirect.com/science/article/pii/S2213158215000856 where gyrification index (GI) is indicated in 'mm'. By definition GI is the ratio of two quantities: inner contour/outer contour (http://en.citizendium.org/wiki/Gyrification) therefore, shouldn't GI be 'unitless' then? I am not sure which way is this correct? Thanks.

2 2

the comand of 'segmentHA_T1_long.sh' is not found
by Gong, Liang 22 Dec '17

22 Dec '17

Hi, I just completed a longitudinal stream preprocessing job using Freesurfer5.3, and I want to further analysis on hippocampal subfields. I see the manual in the following link: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… .but<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…> I can’t find the command of “segmentHA_T1_long.sh”. And then, I change my freesurfer to 6.0, this command also don’t exist. I also try to using “longHippoSubfieldsT1.sh” to do my job, but there is an error when running: ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file. PS：I did my freesurfer job on martinos center, the path is /usr/local/freesurfer/stable6/bin/freesurfer Thanks a lot. Gallen

2 1

[Re] medial wall label in Freesurfer 6
by M del Mar Velasco 22 Dec '17

22 Dec '17

Hi, I am sorry for insisting, but I have found a new mistake in your new version of make_average_surface. rh.medial_wall.label contains 13733 vertex, it is a desired result. However, rh.cortex.label contains all 163842 vertex, i.e, it covers medial wall area too. That's why we still have the same problem because we want to do statistic tests just over the cortex (without medial wall). It also happens with left hemisphere. Could you please take a look at that issue? Thanks very much, M del Mar

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