[Freesurfer] Measuring cortical thickness

Dear Sir / madam, I have 50 subjects (25 healthy controls and 25 patients with BLVP) , I would like to know how could i generate cortical thickness maps for multi subject group analysis. The initial pre-processing with recon-all takes several hours for single subject, is there any alternate way

[Freesurfer] Obtaining White and pial surface maps for multiple subjects

Dear sir, I would like to know how could i possibly generate white and pial surface data for pool of 50 subjects ( 25 healthy controls and 2 subjects with BLVP) using free surfer. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.ed

[Freesurfer] wmparc parcellation for thalamus and brainstem

Dear all, After running through recon-all ,I have obtained wmparc parcellation file (see the attached figure ). I would like to obtain parcellation at specific regions of interest for my study i.e Brain stem region and Thalamus region, could you please let me know how i could perform parcellati

[Freesurfer] rfMRI and T2w image

Dear Sir, In order to run my structural analysis pipeline , i require T2w images, but unfortunately we have not performed T2w scans , my colleague suggests we can use rfMRI instead T2w images Could you please let me know if i can use rfMRI image instead of T2w image?. Thanks Vasudev ___

Re: [Freesurfer] rfMRI and T2w image

Dear sir, I was checking for your reply about my question in Freesurfer Forum but unfortunately i could not your answer although ":Freesurfer Digest, Vol 150, Issue 43 " Today's topics section indicates that you have replied to my question. Following is my question : In order to run my structur

[Freesurfer] Recon-all GNU parallel Error. : Segmentation fault

Dear Sir / madam, I have tried running recon-all with GNU parallel and i am incurring following error kindly review the recon-all.log ( see below ). Could you please let me know why such problem persists for me. Is it the issue with memory space ? Thanks Vasudev Calling the GNU parallel in t

[Freesurfer] Recon-all GNU parallel Error. : Segmentation fault

Dear Sir / madam, I have tried running recon-all with GNU parallel and i am incurring following error kindly review the recon-all.log ( see below ). Could you please let me know why such problem persists for me. Is it the issue with memory space ? Thanks Vasudev Calling the GNU parallel in t

[Freesurfer] Calculating IntraCranial Volume (ICV) for multiple subjects

Dear all, I would like to like obtain the data values of IntraCranial Volume (ICV) for 10 subjects , i know that recon-all automatically calls mri_segstats, but i would like to know if there is any other method to obtain ICV quickly, since running recon-all on each subject takes a lot of time.

[Freesurfer] Calculating IntraCranial Volume (ICV) for multiple subjects

Dear all, I would like to like obtain the data values of IntraCranial Volume (ICV) for 10 subjects , i know that recon-all automatically calls mri_segstats, but i would like to know if there is any other method to obtain ICV quickly, since running recon-all on each subject takes a lot of time.

[Freesurfer] Group analysis Cortical Thickness

Dear Freesurfer Group, I would like to perform group analysis for 50 Subjects (25 healthy controls and 25 Subjects with BLVP ) and examine the changes in cortical thickness between 2 groups, could you please kindly inform me some methods that i should adapt to perform the analysis. Thanks Vasud

[Freesurfer] Converstion of Wavefront .obj files into Nifti

Dear all, Could you please suggest me some method where i can possibly convert Wavefront .obj files into Nifti files, is such conversion technically relevant ?. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

[Freesurfer] Surface based analysis for hippocampus subfield thickness

Dear all, Is there any approach that you recommend to quantify that changes in cortical thickness in hippo campus sub fields , how could i perform Surface based cortical thickness changes using freesurfer. Thanks Vasudev ___ Freesurfer mailing list Fre

[Freesurfer] Cortical thickness changes in Hippocampus sub fields

Dear all, I would like to perform Group ROI analysis between healthy controls and BVF patients where i would like measure cortical thickness changes between healthy controls and BVF, what changes should i adopt to my initial preprocessing tasks using recon-all in order to evaluate changes in cor

[Freesurfer] Talairach Registration Error : recon-all -s

Dear FreeSurfer Developers, I am incurring Talairach registration error when i was running recon-all -s Error : recon-all -s KON2 exited with ERRORS at Do 16. Feb 16:23:10 CET 2017 Freesurfer Version : freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP Platform: Ubuntu 16.04 recon-all log

[Freesurfer] lh.white.H , Failed to create

Dear all , I have been incurring lot of problems while running recon-all on ubuntu 16.04 , recon-all throws following error : " #@# Curv .H and .K lh Sa 25. Feb 04:09:16 CET 2017 /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/surf mris_curvature -w lh.white.preaparc total integra

[Freesurfer] [FSL] Re Orient image from AP to PA axis

Dear all, I would like to if there is any procedure to reorient the image ( flip ) from AP axis to PA , I have around 50 scans all of which are scanned in A/P axis and i would like to reorient them , kindly please let me know if there is any procedure. I tried mri_convert and orient_mri is freesu

[Freesurfer] mri_concat to perform average cortical thickness & pial surface

Dear all, I have 115 subjects , and I would like to perform average cortical thickness ,pial surface . I have used mri_concat for this and i am getting dimension mismatch *" mri_concat k***/surf/lh.thickness --mean --o /media/vasudev/vkirsch4/Data_Driven/Thickness_Pial/lh_thickness/lh.thic

[Freesurfer] Hippocampus subfield segmentation Aborted

Dear all, I am encountering following error when i run Hippocampus subfield segmentation "run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 11266 Aborted "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args ". I am annexing the log file for your notice please kindly revi

[Freesurfer] Cortical Thickness of Hippocampus subfields

Dear Sir, I have performed Subfield segmentation of Hippocampus subfields, I would like to how i can calculate thickness of each subfield post segmentation, are the values in the text files *[lr]h.hippoSfVolumes--.v10.txt*: indicate estimated volume of each subfield , Is there any way i can obtai

[Freesurfer] Generating Mean thickness surface file for volume ROI mask

Dear all, I have a ROI mask volume file and i would like to generate Mean cortical thickness surface file (i.e lh.ROI.thickness.fsaverage.mgh and rh.ROI.thickness.fsaverage.mgh) , could some one guide me how i could obtain such file. I have 120 subjects and I have done recon-all for all subject

[Freesurfer] How to obtain a label for Custom ROI mask

Dear all, I have custom ROI mask ( MNI Space ) that i have prepared from Jülich atlas , I would be like to obtain corresponding surface label file, Could you please guide me necessary the steps that i have to follow inorder to obtain corresponding label for my mask. Thanks Vasudev _

[Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

External Email - Use Caution Dear Sir, I have reviewed your journal which detailed about hippocampus parcellation ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala ) of subfields ( HBT - Head/body/Tail) , could you please let me know how to parti

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

(CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: *Dev vasu > *Date: *Monday, 2 July 2018 at 17:09 > *To: *"freesurfer@nmr.mgh.harvard.edu" , " > igles...@nmr.mgh.harvard.edu&q

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

> Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: *Dev vasu > *Date: *Monday, 2 July 2018

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

External Email - Use Caution Dear Sir, I have another query if i use "export WRITE_POSTERIORS=1", will it generate posterior CA1 and other substructures in the form as cited *posterior_sidev2x.mgz , * Thanks Vasudev On Mon, Jul 2, 2018 at 8:30 PM

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

> > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > -- > *From:* Dev vasu > *Sent:* Tuesday, July 3, 2018 12:22:27 AM > *To:* Iglesias Gonzalez, Eugenio > *Cc:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: Anterior /

[Freesurfer] Problems associated segmentation results of hippocampal subfields

External Email - Use Caution Dear All, I have a problem with the Freesurfer hippocampal longitudinal segmentation results , when i have done segmentation using following algorithm ( https://github.com/CobraLab/antsRegistration-MAGeT) with no anterior/posterior partitioning ( Head/

[Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

External Email - Use Caution Dear All, I have a problem with the Freesurfer hippocampal longitudinal segmentation results , when i have done segmentation using following algorithm ( https://github.com/CobraLab/antsRegistration-MAGeT) with no anterior/posterior partitioning ( Head/

[Freesurfer] recon-all terminated in middle : continuing an analysis of an existing subject

External Email - Use Caution Dear all, I was trying to run recon-all, the pipeline terminated in middle now i would like to know if there is any way i can restart it from the point where it was terminated?. Thanks Vasudev ___ Freesurfe

[Freesurfer] recon-all -make all error

External Email - Use Caution Dear all, I am encountering following error whenever i re-rerun my recon-all on cluster,,although i have downloaded new development version of recon-all.makefile, this error persists,kindly let me know what i am doing wrong recon-all -make all -s /hom

[Freesurfer] Thalamic Nuclei segmentation results

External Email - Use Caution Dear all, I have used Freesurfer pipeline for Thalamic Nuclei segmentation, the results of segmentation appear to be very poor, i am annexing the results , please kindly review if there is any thing wrong with the segmentation results. Thanks Vasude

[Freesurfer] mri_convert : Error while loading library libGLdispatch.so.0

External Email - Use Caution Dear all, I am trying to convert .mgz file to nii.gz using mri_convert command mri_convert filename.mgz filename.nii.gz but i am getting an error "mri_convert: error while loading shared libraries: libGLdispatch.so.0: cannot open shared object file:

[WARNING: UNSCANNABLE EXTRACTION FAILED][Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Transforming Amygdala nuclei atlas to MNI space

External Email - Use Caution Dear all, I am having a difficulty in transforming the segmented subfields of Amygdala atlas from surface based .mgz to nifti format. I have extracted the labels using mri_extract_label lh.hippoAmygLabels-T1.v21.nii.gz 7009 Cortico_amygloid.mgz then

[Freesurfer] Transforming Amygdala nuclei atlas to MNI space

External Email - Use Caution Dear all, I am having a difficulty in transforming the segmented subfields of Amygdala atlas from surface based .mgz to nifti format. I have extracted the labels using mri_extract_label lh.hippoAmygLabels-T1.v21.nii.gz 7009 Cortico_amygloid.mgz then

[Freesurfer] recon_all cuda 9.1

External Email - Use Caution Dear all, Does recon_all -use-gpu only works for CUDA 5.0, is there any way to make it work for CUDA 9.1. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvar

Re: [Freesurfer] recon_all cuda 9.1

source is now compiled with C++ compilers, and I don’t know that > anyone has tried building with cuda since we changed the compilers for > freesurfer. > > - R. > > On Aug 30, 2019, at 11:39, Dev vasu > wrote: > > External Email - Use Caution > > Dear all, > &

[Freesurfer] Convert nifti atlas into .annot file

External Email - Use Caution Dear all, How can i create .annot files for both left and right hemisphere from nifti atlases http://www.gin.cnrs.fr/en/tools/aal/ are there any specific guidelines or commands for surface based parcellation ? Thanks Vasudev

[Freesurfer] How to fasten recon-all execution time without using CUDA

External Email - Use Caution Dear all, I am using - openmp 30 to run recon-all, i see now change in the execution time period. Could you please highlight me a method to reduce the execution time for recon-all, if possible some parallel script to do that same. Thanks Vasudev ___

[Freesurfer] talairach.m3z not found

External Email - Use Caution Dear all, When i run recon-all , i am encountering an error transforms/ talairach.m3z not found during registration phase, could some one please let me know how to resolve this?. Thanks Vasudev ___ Freesurfe

[Freesurfer] CUDA 9.1 with freesurfer

External Email - Use Caution Dear HCP team , Could you please let me know how i can configure CUDA 9.1 with freesurfer 6.0 or Freesurfer 5.3.0 -HCP It is taking a long time by using openmp to run recon-all. please let me know if you have any suggestions for parallelization. Th