Freesurfer

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21 participants
30070 discussions

WM Hypointensities
by Andrew Dedinas Geoly 20 Jul '23

20 Jul '23

External Email - Use Caution Hi Freesurfer experts! I am hoping to extract the wm-hypointensity data from some recon-all-clinical runs. I was able to extract aseg.stats information correctly but noticed there was no information regarding the wm-hypointensities. Is this supported by recon-all-clinical? Best, Andrew --- Andrew D. Geoly, MS Research Data Analyst 1 Brain Stimulation Lab Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine

3 5

Calculate cortical thickness of a volumetric ROI
by Carlos Alcocer 20 Jul '23

20 Jul '23

External Email - Use Caution Hello, I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using https://secure-web.cisco.com/1Z5OP8XDp2iTZo4YMybrzCFH9SwKBzyQx9vsSEFhl_f6qf… as a guide. Since, I already have the volumes in subject space. I did a modified pipeline and only did the following for each subject: 1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh 2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt Does this make sense? Also, separately, is the volume that is also computed in this method accurate? I noticed that the volume is always equal to the number of voxels, which I assume a voxel is equal to 1mm^3? However, when looking at aseg.stats these volumes have different values from their number of voxels. Thank you, Carlos

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Aparc2aseg citation
by Alberto Del Cerro Leon 20 Jul '23

20 Jul '23

External Email - Use Caution Hi FS team, for my line of research I have used aparc2aseg with the --labelwm --hypo-as-wm option to obtain wm measurements from a custom atlas of the brain lobes. However I don't know how I should cite this method as the aparc2aseg documentation does not specify. Thanks in advance

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conjunction analysis stats
by Maria Czarnecka 20 Jul '23

20 Jul '23

External Email - Use Caution Dear Sisters and Brothers in neuroscience, I have a problem with conjunction analysis. I do my analysis using: *mri_concat --i con1/sig.nii.gz --i con2/sig.nii.gz --min --o con.nii.gz* I get a nice map, there are clusters. What about the multiple comparison correction? Maybe I should do the conjunction on the already corrected maps? I would also like to get the cluster table for this conjunction. I tried: mri_surfcluster and it gives me Found 0 clusters and does not save anything. I will be grateful if you help me find the problem. Kind regards, Maria Czarnecka

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Re: [Freesurfer] Pial and White surface maps are not found
by fsbuild 20 Jul '23

20 Jul '23

External Email - Use Caution  Hello Varun, The Windows file system, i.e., NTFS, does not support soft links.  So you cannot set SUBJECTS_DIR to storage mounted from your Windows machine that has been formatted by Windows OS, and then run something in the linux VM that is going to try to write and create a soft link there, e.g., if that is what /media/sf_VBOX/T1_FreeSurfer is set to point to via SUBJECTS_DIR.   Anything that writes and creates a soft link running in the linux VM needs to write directly to the linux file system inside the VM. - R. On Jun 21, 2023, at 11:55, Varun Chandran <varunchandran28(a)gmail.com> wrote:        External Email - Use Caution        p.s. I am wondering whether this specific issue arises while working with freesurfer using Linux based Virtual Machine? On Wed, Jun 21, 2023 at 4:47 PM Varun Chandran <varunchandran28(a)gmail.com> wrote:Hi  YujingThank you very much for your quick reply. Yes, I used a directory path to set an environment variable (SUBJECTS_DIR=/media/sf_VBOX/T1_FreeSurfer) before running the 'recon-all' command line. However, it was not very helpful to obtain the pial and white surface maps and exited with some errors as shown in the recon-all.log (please see the file attached). Now, I'll try running the same command by entering the full path name of the directory as you suggested.                                                                                                                                 thanks again,best,VarunOn Wed, Jun 21, 2023 at 4:13 PM Huang, Yujing <YHUANG43(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Hi Varun, I’m not sure what issue that you have been running into. Can you send your recon-all.log? In general, you need to1. set environment variable SUBJECTS_DIR to some directory that you have write permission2. pass full path to T1 image to -i <full_path_to_T1_image> Best, Yujing  From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Varun ChandranSent: Wednesday, June 21, 2023 10:32 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Pial and White surface maps are not found         External Email - Use Caution        Hi FS experts, It's been a few years, I used FS tools for cortical surface reconstruction. Now, when I used the freesurfer 7.2 version to perform cortical surface reconstruction on the T1-weighted structural MRI data, I was unable to obtain the lh/rh.pial and lh/rh.white surface maps. Can anyone please shed some light on this issue? command line used: recon-all -s T1_260423 -i T1_260423 -all -qcache                                                              thanks, best,Varun -- Varun Arunachalam Chandran, PhDPostdoctoral Research Associate,Faculty of biology, medicine and health,School of health sciences,University of Manchester,United Kingdom.MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1paAi-ZpIjFc28BcfldAkIvpne_JXV1wSSTxNf… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZXw_kqqZ3KZ69Di0XOLR2y7cRSFo0QTVxLkue… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1oLoAtw1TpZh6szgfCA5qRM4stI7vUsPUnYCur…; .-- Varun Arunachalam Chandran, PhDPostdoctoral Research Associate,Faculty of biology, medicine and health,School of health sciences,University of Manchester,United Kingdom.MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1i4aoGzHc6a0AY8hqw5Q4UmY5qB-iVj7FH4bDe… Arunachalam Chandran, PhDPostdoctoral Research Associate,Faculty of biology, medicine and health,School of health sciences,University of Manchester,United Kingdom.MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1paAi-ZpIjFc28BcfldAkIvpne_JXV1wSSTxNf… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_segstats dimension mistach
by Fahad Hannan 20 Jul '23

20 Jul '23

External Email - Use Caution Hello, I'm trying to run the mri_segstats on different input volume. The input volume has the same dimensions as the original volume used to perform recon-all. However, when trying to use the following command: "mri_segstats --seg $SUBJECTS_DIR/P6V1/mri/wmparc.mgz --sum $SUBJECTS_DIR/P6V1/stats/T2lobestest.stats --id 3201 4201 3203 4203 3204 4204 3205 4205 3206 4206 3207 4207 --in T2_Map.nii.gz --in-intensity-name norm --in-intensity-units MR --etiv --subject P6V1 --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt" I get a dimension mismatch error: ERROR: dimension mismatch between input volume and seg input 112 112 80 seg 256 256 256 Seems like during the recon-all process, freesurfer changed the dimensions of the segmentation file to 256 256 256. Is there a way I can resample the segmentation file to the input files dimensions, I know I can resample the input to the norm.mgz file but I do not want to tamper with the input file. Thanks, Fahad

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Problem accessing Buckner40 dataset
by vinuyan sivakolunthu 20 Jul '23

20 Jul '23

External Email - Use Caution Hello Freesurfers, I was trying to access the Buckner40 dataset. There is a fswiki page (https://secure-web.cisco.com/1ErZy9Sg7G0YZ9UZZX83Rz-_dcAsmHYvah0YuvSE1eQCjA…) that points to http://secure-web.cisco.com/1pATPjOdSJnK9tKEHQFm0-GAYffJ_TPyPC3Y39dGCwhvYhQ…, but the site is no longer up. Is there somewhere else where I could obtain the data? Thanks, Vin

2 1

Some bugs in FreeSurfer 7.2.0
by 周乐晴 20 Jul '23

20 Jul '23

External Email - Use Caution Dear Sir, I can find Visual_v3_d cortex area in FreeSurferColorLUT.txt.  but I was confused that where I can find the result file of the visual cortex, or it needs more process?                                                                         Sincerely                                                                        Rosie Zhou  

2 1

free surfer gets stuck during recon-all
by Rona Haker 20 Jul '23

20 Jul '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to do a full brain segmentation for a subject in my study using recon-all but after hours of running it did not reach the final step of creating aparc+aseg (the file I need), even though no error was printed. The last file that was created was 14 hours ago (till I stopped the run manually just now). my command is: recon-all -s ./00_FSseg -i ./8_t1_mp2rage_sag_p3_iso_UNI_Images/004933_t1_mp2rage_sag_p3_iso_UNI_Images_1.dcm -openmp 8 -all Attached is the log report of the run. By the way, this is a subject I have tried 3 times already to segment with no success, although most subjects in my study succeeded on the first try. recon-all -version command outputs this: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Thank you, Rona Haker

2 1

ill conditioned matrix
by 조상아 20 Jul '23

20 Jul '23

External Email - Use Caution I attached fsgd, matrix and error captured file I don't know why this error occurs.

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