Freesurfer

freesurfer@nmr.mgh.harvard.edu

10 participants
30079 discussions

manual segmentation
by 刘卫 27 Oct '21

27 Oct '21

External Email - Use Caution Hello FreeSurfer Developers, I would like to ask, on free surfer, can I directly analyze the data that I run automatically? Do I need to perform manual segmentation again? Thanks!

2 1

orig/001.mgz to brain.mgz transformation?
by Billah, Tashrif 27 Oct '21

27 Oct '21

Hi, 1. What is the name of the space of wmparc.mgz? I see that it is in the same space of brain.mgz. 2. What transform file brings orig/001.mgz to brain.mgz? Best, Tashrif

2 1

recon-all missing files
by Alireza Karami 27 Oct '21

27 Oct '21

External Email - Use Caution Hello I used the following command to create the surface of my subject: recon-all -s subj -i anat.nii -all -qcache -3T However, some files are missing for some subjects. The missing files are .asc files inside the surf folder and COR-001, COR-002, ... inside the orig folder in mri. I used the same command to create the surface of all subjects, but I do not know why the above files are missing for some of them. All the best, Ali

3 2

ERROR: niiRead(): error opening file
by g.toniol＠libero.it 27 Oct '21

27 Oct '21

External Email - Use Caution Hello FreeSurfer Developers, Thank you for your work ! I am trying to segment .nii images with FS, using an ubuntu shell in Windows 10. When I run the command "recon-all" I receive the Error message that the file "exists but is not readable". So I tried converting the file with mri_convert but the following error appears: "niiRead(): error opening file". I tried selecting several different .nii files from different subjects but the same errors appear, I think it is unlikely that all files are corrupted: what may be the cause? I am new to Freesurfer and I apologize if my question is naive but I cannot find a solution in any of the online resources. Thank you very much for your time! Best regards. ________ $ recon-all -s S001 -i /usr/local/freesurfer/7-dev/ws44891-153636-00001-00192-1.nii ERROR: /usr/local/freesurfer/7-dev/ws44891-153636-00001-00192-1.nii exists but is not readable $ mri_convert /usr/local/freesurfer/7-dev/ws44891-153636-00001-00192-1.nii S001/mri/orig/001.mgz ERROR: niiRead(): error opening file /usr/local/freesurfer/7-dev/ws44891-153636-00001-00192-1.nii

2 1

Hard Failures with recon-all
by Wacker, Ewa Helene 27 Oct '21

27 Oct '21

External Email - Use Caution Hello FreeSurfer Developers, for my project I am using Freesurfer 7.1 to examine the hippocampal volumes of patients with major depressive disorder (and controls) using the automatic segmentation. Therefore I have ran recon-all on all the 242 subjects. 12 of them did exit with an ERROR in form of a hard failure. I had troubles finding enough information online on how I could try to fix them by myself. The reports state the following: * for 2 subjects " 3d Normalization pass: could not read source volume brain.mgz\00" - example is subject AIDAB_2017_T1 * for 9 "could not find enough control points" example is subject AIDAB_3097_T1 * for 1 "MRI_watershed Error: global Region of the brain empty" example is subject AIDAB_4007_T1 Is there any chance that there will be a way to include some of the subjects? If needed, I would be happy to send more recon-all.log files, I attached one of each group to this email. Thank you for your time and support, Best regards, Ewa Helene Wacker

2 1

ALL atlas and FS-FAST
by stdp82＠virgilio.it 26 Oct '21

26 Oct '21

External Email - Use Caution Hi is possible to use the AAL for connectivity analysis with FS-FAST? How can I segment the subject GM according with the labels listed in the ALL atlas? Thanks

2 1

Issue with study
by Sarkis, Rani A.,M.D.,M.SC. 26 Oct '21

26 Oct '21

Hello all, I have an issue with a study, and am wondering whether it can be fixed. Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c I am getting a bad talairach output message and when I try to address it with tkregister2 it seems that the orientations are off with coronal sections being treated as sagittal. I assume there is an issue with acquisition. The raw data through freeview looks Ok. all the best, rani

2 1

Converting volume to annotation
by Lorenzo Pini 25 Oct '21

25 Oct '21

External Email - Use Caution Dear experts, I created a modified version of aparc+aseg.mgz files. Values now represent the functional connectivity strength of each parcel in the Desikan-Killiany atlas (ranging from -0.2 to 1 - rvalues). I would like to represent these new parcellation r-values over the native inflated surface (with freeview maybe?). How can I convert this volume (modified aparc+aseg - in orig.mgz space) to label/annotation to be represented on the surface? Thanks!

2 1

trouble accessing Allen Atlas recons
by Budhdeo, Sanjay 25 Oct '21

25 Oct '21

External Email - Use Caution Hi FreeSurfer community, I’m trying to download the Allen Brain Atlas surface reconstructions at this webpage: https://secure-web.cisco.com/17v_p574C0gbjPcUGcI-1oAdpOuTLVkcnkI9eEapnGbJob… Unfortunately I haven’t been able to the download the file. I’ve tried the following mitigation steps : - trying to download using (FreeSurfer v5.3 recons<ftp://surfer.nmr.mgh.harvard.edu/pub/data/AllenBrainFreeSurferv5.3.tar.gz>) in Safari and Firefox - using a home and university connection - using a download manager - using Cyberduck for ftp access to the file I’d be grateful for any advice on how to download the recons! Many thanks, Sanjay Budhdeo

1 0

Re: [Freesurfer] long_mris_slopes
by Veena Nair 22 Oct '21

22 Oct '21

External Email - Use Caution That worked! *python2 /opt/softwarepackages/freesurfer/bin/long_mris_slopes --qdec qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time months --qcache fsaverage --sd $SUBJECTS_DIR* Thank you!

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