Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

Correct for sulcuses & ventricles size
by John Anderson 13 Dec '20

13 Dec '20

External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space between the sulcuses and the size of ventricles. My questions are: 1. Is there any way to correct for these differences in the surface based analysis? 2. Including eTIV covariate does it help in this case? 3. Does the resampling to "fsaverage" overcome the challenge of these differences between the subjects? I appreciate any advice, John

3 5

Extract he value of area and volume in the fsaverage for every subject
by 李梦君 07 Dec '20

07 Dec '20

External Email - Use Caution Dear FreeSurfer Developers: I compared the cortical thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area and volume after correction. How can I extract the value of cortex area and volume for every subject in the fsaverage with the code of mri_segstats FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS High Sierra. Best wishes Mengjun Li Second Xiangya Hospital Central South University

3 20

Re: [Freesurfer] extracting beta coefficients and p-values
by Batool Rizvi 29 Nov '20

29 Nov '20

External Email - Use Caution Hi, I had a couple additional questions related to this topic. 1. The beta-coefficients I derived from using the mri_segstats command with the input beta.mgh, are these values unstandardized? 2. Just wondering, is there a possible way to also derive 95% confidence intervals for my covariates that were included in the mri_glmfit analyses? Thanks so much for your help! Batool

3 5

recon-all 7.1.1
by James Hartzell 27 Nov '20

27 Nov '20

External Email - Use Caution Hi Andrew Thanks for the suggestions. I removed freesurfer and reinstalled just 7.1.1. When I try to run the original patch you suggested I still get permissions problems, even with sudo. (base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer /Applications/freesurfer/7.1.1/bin/freesurfer (base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd $FREESURFER_HOME/bin (base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all recon-all.backup Password: (base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/reco… > recon-all zsh: permission denied: recon-all Here's hoping you can send another fix! Cheers James -- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

2 11

recon-all for 0.85 isotropic images error
by Lee Subin Kristine 18 Nov '20

18 Nov '20

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to run recon-all (v.6) on T1- and T2-weighted images that have 0.85mm^3 isotropic voxels I have entered the command as below, with the T2, T2pial, cm, cw256 flags. recon-all -i $T1_DIR/"oT1_"$subj.nii -T2 $T2_DIR/"oT2_"$subj.nii -T2pial -cm -cw256 -subject $subj"_test" -all However, I keep getting the error as follows. ERROR! FOV=272.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. I'm guessing that conforming to the small voxel size results in a FOV that is out of limit? However, when I check the orig.mgz file it looks fine. (It has an image dimension of 320 x 320 x 320). Even when I include the flag -cw256 as the error message says, I still get the same error message. (Also, I cannot find any documentation about the -cw256flag on the help page). I have pasted the full log below. Thank you for your help. Best regards, Kristine ------------------------------------------------------------- subin@ubuntu:/mnt/hgfs/subindata/MYELIN-QSM/SCRIPT$ ./run_fs_1 INFO: all volumes are conformed to the min voxel size Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW Actual FREESURFER_HOME /usr/local/freesurfer Linux ubuntu 4.15.0-112-generic #113~16.04.1-Ubuntu SMP Fri Jul 10 04:37:08 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/scripts/recon-all.local-copy' -cw256 option is now persistent (remove with -clean-cw256) /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test mri_convert /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz mri_convert.bin /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99998, -0.00515189, -0.00357438) j_ras = (0.00515192, 0.999987, 0) k_ras = (0.00357433, -1.83865e-05, 0.999994) writing to /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Fri Oct 30 05:19:16 PDT 2020 /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test mri_convert --no_scale 1 /mnt/hgfs/subindata/MYELIN-QSM/BRL_T2/oT2_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/T2raw.mgz mri_convert.bin --no_scale 1 /mnt/hgfs/subindata/MYELIN-QSM/BRL_T2/oT2_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/T2raw.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/hgfs/subindata/MYELIN-QSM/BRL_T2/oT2_BRL_0004.nii... TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99998, -0.00515189, -0.00357438) j_ras = (0.00515192, 0.999987, 0) k_ras = (0.00357433, -1.83865e-05, 0.999994) writing to /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Fri Oct 30 05:19:23 PDT 2020 Found 1 runs /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test mri_convert /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig.mgz --conform_min mri_convert.bin /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99998, -0.00515189, -0.00357438) j_ras = (0.00515192, 0.999987, 0) k_ras = (0.00357433, -1.83865e-05, 0.999994) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig.mgz... **************************************** ERROR! FOV=272.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux ubuntu 4.15.0-112-generic #113~16.04.1-Ubuntu SMP Fri Jul 10 04:37:08 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BRL_0004_test exited with ERRORS at Fri Oct 30 05:19:38 PDT 2020 For more details, see the log file /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 3

surf pial_lgi not created in version 7.1.0
by Kathy L. Pearson 16 Nov '20

16 Nov '20

External Email - Use Caution In freesurfer version 5.3.0, I can successfully run: recon-all -autorecon-all -mprage -s $subj -qcache -localGI recon-all -s $subj -qcache -measure pial_lgi However, the same commands with 7.1.0 give an error after this last of a number of generated statements and no surf/*pial_lgi output: mris_preproc --s 147608 --hemi lh --meas pial_lgi --target fsaverage --out lh.pial_lgi.fsaverage.mgh nsubjects = 1 ERROR: cannot find subjects/147608/surf/lh.pial_lgi Is a new command needed for version 7.1.0? Thanks, Kathy Pearson

2 7

please help me
by saman fouladi 11 Nov '20

11 Nov '20

External Email - Use Caution hi I want to process MRI images to extract Morphology features. I convert my dcm file to nii format by mri-convert command and then I used FSL software and BET(Best extraction Tool). Next I do not know what to do to extract morphological features? My other question is what is the difference between recon-all and use FEAT( in FSL software)? What are the uses of each? Thank you

4 14

Fixing error with pial surface
by Julie Ottoy 06 Nov '20

06 Nov '20

External Email - Use Caution Dear Freesurfer team, I have a question related to fixing the pial surface when a part was missed (see attachment). On the freesurfer website, I only found how to erase the pial when there was too much (see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEditsV6.0 ), but I could not find what to do when there was too little. As there is no white matter in this particular area, it is also not an option to place control points. Also the skull stripping did not change anything: I tried both the freesurfer skull stripping and an in-house skull stripping algorithm. Thank you for your help. Best regards Julie

3 8

MRI SNR
by 南修司郎 06 Nov '20

06 Nov '20

External Email - Use Caution Dear expert We are planning multi-center study with the hearing impaired patients using FreeSurfer. The signal-to-noise ratio (SNR) of the test MRI from a center does not look very good, but the FreeSurfer can analyze the gray matter. How much the allowable SNR for FreeSurfer analysis? This is the MRI protocol and the test image. Thank you in advance. Shujiro Siemens MAGNETOM Altea 1.5T Voxel size 1.0X1.0X1.0mm3 Geometry 　 FOV 256mm(256X256 matrix) Slice 176 Orientation sagittal Slice thickness 1mm Phase Encoding Dir A→P Timing 　 TR 2730 TI 1100 TE 1.64/3.59/5.36/7.31 bandwidth 651 RF 　 Magn.Preparation Non-sel.IR FA 7° Acceleration GRAPPA 　 Acceleration Factor PE 2 Reference Line PE 32 Slice Partial fourier 6/8 ScanTime 6:08 Shujiro Minami M.D., Ph.D. Dpt. of Otolaryngology National Tokyo Medical Center 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan E-mail shujirominami(a)me.com

2 1

trac-preproc error
by Hasimoglu, Yasemin 05 Nov '20

05 Nov '20

Hi, I'm running Tracula on a longitudinal dataset and it's failing at the preproc stage for one subject with the following message: INFO: Distances between consecutive points in test subject's space are 16 13 12 14 WARN: Could not find satisfactory control point fit - try 4967 Finding center streamline INFO: Step is 3 voxels WARN: Turning off deviation check for center streamline INFO: Step is 3 voxels WARN: Turning off FA check for center streamline INFO: Step is 3 voxels WARN: Turning off overlap check for center streamline INFO: Step is 3 voxels WARN: All checks already off. Exiting. Selecting 5 points on center streamline ERROR: Selected streamline has fewer than 5 points Linux zorii.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Oct 28 04:11:51 EDT 2020 It looks like the problem is with one specific pathway. I checked the brainmask and the inter and intra-subject registrations and they all look fine to me, so I'm not sure what else to check. The trac-all.log file is quite large, I attempted to attach it in this email several times, but it always gets rejected, so I'm not attaching it for now. I would greatly appreciate any advice! Best, Yasemin

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Freesurfer October 2020