Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Average hemispheric R1 value
by Damien MARIE 01 Jun '17

01 Jun '17

Dear experts, I would like to extract the mean left / right R1 value for each of my subjects (R1 = 1/T1). I did that with mris_anatomical_stats (see below) and I’m assuming that “ average cortical thickness = 0.001 mm +- 0.000 mm “ is my average R1 value (in that case for the right hemi). Is that correct? Now I would like to get my average hemi R1 value with 5 decimal numbers if possible because R1 values are very low, for instance in the same subject considering the whole brain average R1 is equal to 0.000737 . Is it possible ? Thank you and best, Damien mris_anatomical_stats -t rh.R1.mgh ct_pp2_N4_bet_MP2RAGEcorr rh outputting results to R1file... using thickness file rh.R1.mgh. reading volume /home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/mri/wm.mgz... reading input surface /home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.white... Using TH3 vertex volume calc Total face volume 293919 Total vertex volume 289553 (mask=0) reading input pial surface /home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.pial... reading input white surface /home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.white... structure is "/home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.white" number of vertices = 148874 total surface area = 103857 mm^2 total gray matter volume = 289553 mm^3 average cortical thickness = 0.001 mm +- 0.000 mm average integrated rectified mean curvature = 0.136 average integrated rectified Gaussian curvature = 0.030 folding index = 2174 intrinsic curvature index = 190.6

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Contrast matrix format
by Taylor Hilton 01 Jun '17

01 Jun '17

Hi all, I’m trying to perform a group analysis according to the tutorial on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> For my own analysis, I have 4 total groups, and I’m trying to do a contrast between two of those groups. My matrix file is formatted ‘0 1 -1 0’, since I’m trying to contrast the 2nd and 3rd groups. My fsgd file is formatted as the following: GroupDescriptorFile 1 Title PYSCan Class 1 Class 2 Class 3 Class 4 Input s70032 2 Input s70038 1 … Wanted to verify that this is correct since there doesn’t appear to be a group difference when comparing the clusters against the rest of the data. Any help is very appreciated! Sincerely, B. Taylor Hilton Lab Data Coordinator University of Pittsburgh

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How to process ANCOVA with age as covariate
by Gwang-Won Kim 01 Jun '17

01 Jun '17

1 0

recon-all errors
by Maria Economou 01 Jun '17

01 Jun '17

Dear FreeSurfer developers, I am new to using the software, so forgive me if my mistake is something very basic! I've been trying to do recon-all for my first subject and I keep getting several errors like: ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 Too many open files ERROR: reading /Applications/freesurfer/FreeSurferColorLUT.txt Loading pixel data ERROR: /Applications/CONTROLS/147364_Nd_19760623/IM-0001-0001.dcm is not a dicom file 70092 Requested element (18 82) not found in DCM_GetElementVM I have used the DICOM files from my 3D T1 MPRAGE SENSE images. This is the command i used: uos$ recon-all -subjid 147364 -i /Applications/CONTROLS/147364_Nd_19760623/IM-0001-0001.dcm -all FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c platform: OS X El Capitan Version 10.11.6 Please find attached the recon-all.log Many thanks, Maria.

1 0

label file from freesurfer 5.3
by Daniel Yang 31 May '17

31 May '17

Dear FreeSurfer experts, When I tried to use FreeSurfer 6.0.0’s freeview to open a label file generated by FreeSurfer 5.3, I could not see anything. Is it incompatibility issue going on here? Thanks, Daniel

2 8

Mapping Vertices from Subject to MNI using mri_label2label
by Hengda He 31 May '17

31 May '17

Hi Freesurfer Developers, I'm trying to map the vertices of entorhinal cortex(EC) in one subject into the space of MNI152 by using mri_label2label. 1) The vertices of EC from subject were extracted using: mri_annotation2label --subject FreeSurfer --hemi lh --labelbase FreeSurfer/Vertices/aparc-lh Those vertices were saved in FreeSurfer/Vertices/aparc-lh-006.label. 2) And I used mri_label2label to map it into the MNI space: mri_label2label --srclabel /FreeSurfer/Vertices/aparc-lh-006.label --srcsubject FreeSurfer --trglabel /FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label --trgsubject FreeSurferMNI152 --regmethod surface --hemi lh So, the mapped vertices were in /FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label 3) I also extracted the vertices of EC from MNI as a reference: mri_annotation2label --subject FreeSurferMNI152 --hemi lh --labelbase FreeSurferMNI152/Vertices/aparc-lh Vertices of EC from MNI were saved in FreeSurferMNI152/Vertices/aparc-lh-006.label. To my understanding, the mapped vertices(/FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label) should cover almost the same surface region as the reference vertices(FreeSurferMNI152/Vertices/aparc-lh-006.label), right? But the reference vertices seem to cover a bigger region, which is shown in the attached picture(Red Points:mapped vertices, Red&Green Points:reference vertices). We are using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and the computer is CentOS release 6.9. Thanks! All the Best, Hengda ----------------- Attachment: 1) terminal output from mri_annotation2label --subject FreeSurfer --hemi lh --labelbase FreeSurfer/Vertices/aparc-lh subject = FreeSurfer annotation = aparc hemi = lh labelbase = /FreeSurfer/Vertices/aparc-lh surface = white Reading surface /FreeSurfer/surf/lh.white Loading annotations from /FreeSurfer/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 max index = 35 ... 6 516 /FreeSurfer/Vertices/aparc-lh-006.label LabelWrite: saving to /FreeSurfer/Vertices/aparc-lh-006.label ... 2) terminal output from mri_label2label srclabel = /FreeSurfer/Vertices/aparc-lh-006.label srcsubject = FreeSurfer trgsubject = FreeSurferMNI152 trglabel = /FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 FREESURFER_HOME /usr/local/freesurfer/5.1 Loading source label. Found 516 points in source label. Starting surface-based mapping Reading source registration /FreeSurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /FreeSurferMNI152/surf/lh.white Reading target registration /FreeSurferMNI152/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 516 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 199 Checking for and removing duplicates Writing label file /FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label 715 LabelWrite: saving to /FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label mri_label2label: Done 3) terminal output from mri_annotation2label --subject FreeSurferMNI152 --hemi lh --labelbase FreeSurferMNI152/Vertices/aparc-lh subject = FreeSurferMNI152 annotation = aparc hemi = lh labelbase = /FreeSurfer/Vertices/MNI-aparc-lh surface = white Reading surface /FreeSurferMNI152/surf/lh.white Loading annotations from /FreeSurferMNI152/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 max index = 35 ... 6 648 /FreeSurfer/Vertices/MNI-aparc-lh-006.label LabelWrite: saving to /FreeSurfer/Vertices/MNI-aparc-lh-006.label ...

2 1

DIAG influencing recon-all pipeline?
by Jens Offenbach 31 May '17

31 May '17

Hallo, first of all: Sorry to be a little bit clingy, but I have some problems in understanding regarding the DIAG option in FreeSurfer. As suggested by Bruce, I have set DIAG to 0xFFFFFFFF and DIAG_VERBOSE to 1. I am getting a lot of output now and a very large recon-all.log. Unfortunately, I am not able to run a recon-all on the OASIS-Brains subject "OAS1_0001_MR1" and "OAS1_0004_MR1" successfully after converting the *.img to *.mgz via mri_convert. I order to get FreeSurfer in the cloud, I have created a minimum archive of FreeSurfer 6.0.0 using strace to monitor all files that are being accessed in the course of recon-all. The archive does not seem to work with DIAG set to 0xFFFFFFFF. I am not sure, but my first guess is that the DIAG option also influences the recon-all pipeline. Is this right? Is there a way to increase the log level without influecing any analysis steps? The whole run takes much longer than a "normal" recon-all without DIAG set to any level. My current run fails with: ... HIPS unsupported No such file or directory Linux neuroimaging02 4.8.0-53-generic #56~16.04.1-Ubuntu SMP Tue May 16 01:18:56 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s OAS1_0001_MR1 exited with ERRORS at Wed May 31 02:54:32 UTC 2017 I will prepare a new run with strace and the original FreeSurfer-archive to check process behavior when DIAG is set to 0xFFFFFFFF. Unfortunately, everything takes so much time... I have a prepared a large test scenario with different hardware constellations to check if the encountered SegFault is hardware on not software related. Thank you very much! Regards, Jens

2 2

Project volumes in MNI to lrsym_fsaverage6
by Meiling Li 31 May '17

31 May '17

Dear freesurfer experts I have processed resting state fMRI data in MNI space , for example: Data: 91*109*91*240, 240 was the time frames number. How could i project the data in MNI space to the symmetric surface(eg lrsym_fsaverage6) ? Thanks in advance! Meiling

1 0

Qdec/Tksurfer keyboard input error
by Victor Montal Blancafort 31 May '17

31 May '17

Dear Freesurfer experts: Recently, I have update my OS to Ubutnu 16.04. Afterwards, I tried to re-run some analysis using Qdec 1.4 (stable 5.1) and Qdec 1.5 (stable 6.0). However, I am not able to input any threshold via my keyboard (neither the Subjects or Display tab). This issue also happens when I try to use tksurfer. I have seen several posts regarding this issue in the mail-list, but none of them received any answer. Any insight would be really appreciated. Thank you in advance, Victor M.

1 0

mri_annotation2label No such file or directory
by Duy Nguyen 30 May '17

30 May '17

Dear FreeSurfer experts I am trying to extract the label using standard aparc.annot and will be using mri_mergelabels to create my own lobes to do GLM fit later on for ROI analysis. However, it shows me the error like this when I check there are the files aparc.annot and the file from surf folder. [toibigi2007@localhost OASIS_Data]$ mri_annotation2label --subject OASIS_0002_MR1 --hemi lh --outdir $SUBJECTS_DIR/OASIS_0002_MR1/label subject = OASIS_0002_MR1 annotation = aparc hemi = lh outdir = /media/3B110EAE3B9DE8E0/OASIS_Data/OASIS_0002_MR1/label surface = white ERROR: creating directory /media/3B110EAE3B9DE8E0/OASIS_Data/OASIS_0002_MR1/label No such file or directory One more question is that it says default is "white" surface, but I want to measure the cortical thickness. Can I leave white in like this or do I change into --surf to gray for this? Thank you and best regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme(a)gmail.com <duy.nguyenbme(a)gmail.com>*

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