Freesurfer September 2021

freesurfer@nmr.mgh.harvard.edu

76 participants
107 discussions

Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG
by Donatas Sederevicius 28 Aug '22

28 Aug '22

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method. https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1

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Tracula 7.2 using older structural outputs
by Alexopoulos, Dimitrios 21 Nov '21

21 Nov '21

External Email - Use Caution HI, Can you run Tracula 7.2 using older structural outputs generated with FS 6.0 and 7.1.1? Jim ________________________________ 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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Re: [Freesurfer] Base correction, longitudinal analysis
by Eszter Boros 01 Nov '21

01 Nov '21

External Email - Use Caution Thank you for your answer! I think I should clarify this question a little bit. So this is about correcting the Base. And run recon-all *after *correcting the Base. What command should I use here? if I want to regenerate only the Base after correcting it? Because the common below does not work: (ERROR: must specify subjects for base subject using -base-tp) recon-all -base OAS2_0057 -autorecon-pial But if I use "recon-all -base OAS2_0001 -tp OAS2_0001_MR1 -tp OAS2_0001_MR2 -all" that just creates a new Base based on the cross MR1 and MR2. My question is how can I regenerate the corrected Base? What command should I use? Thank you so much! All the best, Eszter Boros Eszter Boros <boros.eszter0226(a)gmail.com> ezt írta (időpont: 2021. aug. 8., V, 19:04): > Dear FreeSurfer Team, > > I am working on a longitudinal pipeline and after correcting the Cross and > generating the Base, I can still see some pial problems sometimes (on the > Base). > > I read on the Freesurfer website that it is possible to correct and > regenerate only the Base, but when I use this command: > > recon-all -base OAS2_0057 -autorecon-pial > > /where OAS2_0057 is the name of the Base/ > > I get the following error message: > > ERROR: must specify subjects for base subject using -base-tp > > > Why is this not working? I am using Freesurefer 7.1.1. > > Thank you so much! > > All the best, > Eszter Boros > >

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Problem with intensity normalization control points
by Staci A Board 18 Oct '21

18 Oct '21

External Email - Use Caution Hello, our lab has been using freesurfer for years, dating back to version 4.3 and recently ran into a problem with a new installation of 7.2. After adding control points in the typical fashion and saving them into the subject’s tmp folder as “control.dat” and running -autorecon2-cp, mri_normalize seems to correctly identify the control points, the correct number, the mean value and the scaling. The subsequent steps complete without failure and brain.mgz is generated with 110 values in the cp spots. However, the subsequent wm.mgz and brainmask.mgz images do not seem to have been affected by the control points (e.g. the control point locations aren’t at a 110 value and the white matter is almost identical). Curious if anyone else has run into the issue? Is there a new workflow in this version of Freesurfer that I’m neglecting? So far I have tried to create a new control.dat using freeview and copied the old points into that file, and run twice with the same results.

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Freesurfer version help
by Annalisa Lella 09 Oct '21

09 Oct '21

External Email - Use Caution Hi, I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0? Thanks a lot for any help you could give to me! Best regards, Annalisa Lella

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Not seeing effects of manual edits and re-running recon-all
by Kevin Miller 08 Oct '21

08 Oct '21

External Email - Use Caution Hi, I am new to recon-all and Freesurfer and I am having some difficulty tracking down the resulting outputs from when I re-run recon-all or they are not taking hold. So far I have edited two subjects after the initial run by lowering the ws height for the skullstrip in one and by adding white matter voxels by in the other. I followed all the tutorial instructions for both, starting with the edits and including the appropriate recon-all commands, which supposedly finished without error. However, after viewing the new volumes that were overwritten the day they were run, neither seem to have changed. For the wm.mgz, even, the wm voxel edits still exist as though recon-all did not run. If anyone has any tips for finding the proper outputs or what I might be doing incorrectly, I would greatly appreciate any advice. Thanks

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glmfit sig file all zeros
by Pedersen, Walker Scott 08 Oct '21

08 Oct '21

Hi, I am running glmfit on some functional data (using ces.nii.gz surface files as input) using ROIs and the --mask argument, that I plan to later submit to glmfit-sim for small volume correction. I have some rois that are subcortical and some that are surfaces. For the glmfit run within the surface ROIs the output sig.nii.gz files all voxels have a value of zero. However, this is not the case for the F.nii.gz and z.nii.gz files output by the same glmfit command - they have non-zero voxels. This issue only occurs for the surface ROIs, when I run glmfit in subcortical ROIs the sig.nii.gz files look normal. The surface ROIs were created by using afnis 3dundump to create 10mm spheres from MNI coordinates. I then ran the MNI template through freesurfer, and used the regheader from this to run mri_vol2surf to put the spherical ROIs into fsaverage space. I am able to view the resulting surface ROIs projected onto the fsaverage surface in freeview, and have checked that my ces.nii.gz function files can also be overlayed onto the same fsaverage template in freeview. The output of one of the glmfit commands in question is below. thanks! WARNING: gdfReadV1: no variables on 'Variables' line found Reading source surface /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/subjects/fsaverage/surf/lh.white gdfRead(): reading /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles/ /fsgd.txt INFO: gd2mtx_method is dods Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 7.1.1 cwd /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast cmdline mri_glmfit --glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lC S+E_m_lCS-atCS+E/outputFiles/lIFG/ --y /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recal l//recall.sm5.lh/lCS+E_m_lCS-atCS+E/ces.nii.gz --surf fsaverage lh --fsgd /autofs/space/uriline_003/users/projects/OC D_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt --C /autofs/space/uriline_003/users/projects/OCD_NM/ walker_pedersen/data/image/main/recall/inputFiles//groupDiff.mtx --nii.gz --mask /autofs/cluster/neuromod/NIFTI/OCD_N M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz --eres-save sysname Linux hostname r440-28.nmr.mgh.harvard.edu machine x86_64 user wsp6 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_lCS-atCS+E /ces.nii.gz logyflag 0 usedti 0 FSGD /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz maskinv 0 glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atCS+E/outp utFiles/lIFG/ IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+ E_m_lCS-atCS+E/outputFiles/lIFG/ Loading y from /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_ lCS-atCS+E/ces.nii.gz ... done reading. INFO: gd2mtx_method is dods Saving design matrix to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_ m_lCS-atCS+E/outputFiles/lIFG//Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1.125 Pruning voxels by thr: 1.175494e-38 Found 512 voxels in mask Saving mask to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atC S+E/outputFiles/lIFG//mask.nii.gz Reshaping mriglm->mask... search space = 222.026773 DOF = 15 Starting fit and test Fit completed in 0.0002 minutes Computing spatial AR1 on surface Residual: ar1mn=0.987586, ar1std=0.043927, gstd=3.620916, fwhm=8.526606 Writing results groupDiff MRImask(): AllowDiffGeom = 1 INFO: MRImask() using MRImaskDifferentGeometry() maxvox sig=-0 F=4.36504 at index 391 0 0 seed=1632900996 mri_glmfit done

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Brodmann areas volumetric parcellation freesurfer 6.0
by Ahmed Radwan 08 Oct '21

08 Oct '21

External Email - Use Caution Dear FreeSurfer experts, I would like to generate .mgz Brodmann parcellation maps in FreeSurfer 6.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) to be precise. Is this possible? I found this thread (https://secure-web.cisco.com/177FKNV88nkCNrwgn4jIC93-E_ZjHSBW0BXiH1uX3pOj28…) asking a similar question but aiming to propagate those parcellations into WM using FS 7.1. Thanks in advance, Ahmed Radwan

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Freesurfer September 2021