Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Qdec factor.levels loading error
by Yu(余)Qijing(奇静) 28 May '14

28 May '14

Dear Freesurfers, I am experiencing the following problem when I load the qdec.table.dat file in qdec: Loading data table /Volumes/fMRI/Scanner_Data/qdec/qdec.table.dat... QdecDataTable::Load: will attempt to open as Mac text file... Number of columns: 4 fsid column: 1 Number of factors: 3 Number of subjects: 89 Reading discrete factor levels from config file /Volumes/fMRI/Scanner_Data/qdec/gender.levels ?? done. ERROR: /Volumes/fMRI/Scanner_Data/qdec/gender.levels is invalid. Must have at least two levels. The discrete factor is gender. I tried adding a new line at the end of both qdec.table.dat and gender.levels files, but still have the problem. I attached the gender.levels. I created both .dat and .levels files in excel, and saved as delimited txt, then forced the extension to be .levels and .dat. Did I do anything wrong when creating them? Also I noticed "QdecDataTable::Load: will attempt to open as Mac text file...", could this mean the error may be from qdec.table.dat file? Thank you very much! All the best, QJ

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recon -all with .nii input problems with perl version 5.18
by Samuel Thorpe 28 May '14

28 May '14

Hello, I recently upgraded from Ubuntu 13.10 to 14.04, and I started getting a new error message while running "recon-all" with .nii file inputs (details below). From the error message I believe the problem might be that Ubuntu 14.04 ships with perl version 5.18 (as opposed to 5.14 for previous versions), and the Ubuntu 14.04 Perl manpage (http://manpages.ubuntu.com/manpages/trusty/man1/perl5120delta.1.html) specifically lists "shellwords.pl" as a newly deprecated library. My naive instinct was to install perl version 5.14 using perlbrew, and switch to it whenever a new shell is launched by editing my .bashrc file, by adding the lines "source ~/perl5/perlbrew/etc/bashrc" "perlbrew switch perl-5.14.4" When I do this my shell recognizes perl-5.14.4 as the active version, but freesurfer does not. This makes me worry it won't be such a simple fix. Any Ideas as to the best way to handle this? Am I on the right track? Many Thanks! -Samuel Thorpe bugr related info: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer SUBJECTS_DIR: /usr/local/freesurfer/subjects "which recon-all" gives "/usr/local/freesurfer/bin/recon-all" Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: jessie/sid Kernel info: Linux 3.8.0-32-generic x86_64 Linux OS: Ubuntu 14.04 LTS "Trusty Tahr" example commands executed: --------------------------------------------------------------------- subject: "bert", "bert_nii" after converting "/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz" to .nii using "mri_convert" (operation successful), I attempt, "recon-all -i /usr/local/freesurfer/subjects/bert/mri/orig/001.nii -s bert_nii -all" error message: --------------------------------------------------------------------- "Can't locate shellwords.pl in @INC (@INC contains: /usr/local/freesurfer/mni/bin/../lib/mni_autoreg /usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/mritotal line 460." /usr/local/freesurfer/subjects/bert_nii/script/recon-all.log attached

2 1

dt_recon error
by Weber, Wade (weberw) 28 May '14

28 May '14

Hi all, I have been trying to work with DTI data in FreeSurfer for the first time. We acquire our data on a 4T Varian and reconstruct into AFNI format (BRIK/HEAD files). I set up the bval and bvec files successfully and ran the "dt_recon" script. It seemed to run fine until I got an fslregister error saying "G-W contrast is negative but expecting positive." It says to try running with the "--T1" flag. The problem is that I'm not sure which line I put the flag into. I tried re-running the dt_recon line again with the --T1 flag, but it did not work. I know I may not be giving enough information, so if anyone needs more information, just let me know what you want to know. Thanks in advance! Wade Weber University of Cincinnati

2 4

mri_vol2vol error "--o: command not found"
by Ben Mooneyham 28 May '14

28 May '14

Hi all, I'm trying to transform a mean functional image into subject (T1) space using mri_vol2vol. Originally, my code worked successfully, but in attempts to re-run the procedure, both on the same data and on additional data, I've encountered an error in which the log reports an "ERROR: Option unknown" and also "--o: command not found." I am hoping to resolve this issue; does anyone see where my issue is arising from? This is especially strange given that I've gotten it to work before, and I don't think I made any changes to the script besides changing the directory locations for different subjects' data. Here is the mri_vol2vol command as I currently have it: mri_vol2vol --reg ${iSub}_bbregister.dat --mov ${iSub}_Tempfiltered_mean.nii --targ ${DataDir}/S1/${iSub}/${iSub}_brainmask.gcuts.nii \ --o ${iSub}_mean_epi_inT1.nii The cd is ${DataDir}/S1/${iSub} , which contains the ${iSub}_bbregister.dat , ${iSub}_Tempfiltered_mean.nii , and ${iSub}_brainmask.gcuts.nii files. Thanks for your help, Ben Mooneyham -- Graduate Student UCSB - Department of Psychological & Brain Sciences Building 429 Room 102 (210) 912-6076 bwmooneyham(a)gmail.com

2 1

extract mean thickness, surface area of ROI
by sabin khadka 28 May '14

28 May '14

Hi all, I want to extract mean cortical thickness, surface area of an ROI I created with some clusters that showed some group difference. I already have the ROIs I need. What is the easiest way to extract mean values of ROI from all the subjects? Thanks, Sabin

2 1

vtk scalars to freesurfer annot
by Ronald Pierson 28 May '14

28 May '14

Does anybody know a straightforward way to take a labeled vtk image and create a freesurfer image with the accompanying annotation file? Or is there a way to create an annotation file from the list of vertices and labels? Ronald Pierson

1 0

long_mris_slopes bug
by Katherine Reiter 28 May '14

28 May '14

Hi Freesurfer experts, I'm working on analyzing longitudinal data using the longitudinal 2-stage model. When running the data through long_mris_slopes, I was getting the following error message: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? I saw in previous messages that this is the result of a bug. I found the fix under the release notes, though after downloading it and placing the fix in the bin and makign these files executable, I keep receiving the following error messages. Does anyone have any insight into the problem and possible solutions? mri_convert --frame 0 ./tmp-0001_base_lh_thickness_3f8Byr/glm/beta.mgh ./tmp-0001_base_lh_thickness_3f8Byr/beta0.mgh Traceback (most recent call last): File "/Applications/freesurfer//bin/long_mris_slopes", line 744, in <module> run_cmd(cmd,'mri_convert split frames 0 did not work?') File "/Applications/freesurfer//bin/long_mris_slopes", line 422, in run_cmd retcode = subprocess.call(args) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 486, in call return Popen(*popenargs, **kwargs).wait() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 672, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1202, in _execute_child raise child_exception OSError: [Errno 8] Exec format error Thank you, Katherine Reiter, M.S. Clinical Psychology Doctoral Student Marquette University Phone: (414) 288-3807 Email: katherine.reiter(a)marquette.edu

2 2

Corpus Callosum segmentation
by Alessia Giuliano 28 May '14

28 May '14

Dear FreeSurfer team, I'm intrested in the segmentation of Corpus Callosum and in the volumes of its subregions. Freesurfer divides the Corpus Callosum in 5 subregions but I have noticed an inconsistency in the boundary that separates the anterior part from the middle anterior one. In particular, the Rostrum is sometimes included in the anterior part, but other times it is included in the middle anterior part, as you can see comparing the two screenshots that I've attached. How much can I consider this parcellation to be reliable? Thank you, Alessia Giuliano

2 3

Registration of Functional Data to the Inflated Brain
by Sherryse Corrow 27 May '14

27 May '14

Hi FreeSurfer Team, Please help out a FreeSurfer newbie! We are having an issue with mapping our functional data onto the inflated brain. When we finish the mapping, it seems that much of the data is showing up in white-matter space, and therefore, cannot be seen on the external surface of the brain. We later discovered that we were likely using the wrong registration matrix. However, it doesn’t seem like the one we are supposed to use is being produced during recon-all. I am new to FreeSurfer and would greatly appreciate some assistance! To provide you with more detail. Problem: When we run the command line below, and then open the folder experiment.feat/reg/freesurfer, there is no anat2exf.register.dat file. However, there is a file called: anat2exf.register.dat.init. Command Line: Reg-feat2anat -feat OurFeatDirectory.feat -subject P143 Terminal Output: There is no terminal output. No error of any kind. Log File: Attached. Thanks, Sherryse P.S. We submitted this issue previously but were not getting a response, so we tried again in case our thread wasn’t working properly. -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.corrow(a)eyecarecentre.org<mailto:sherryse.corrow@eyecarecentre.org>

3 2

Error: no dicom files found
by Caroline Lewis 27 May '14

27 May '14

Hi, I am trying to use the unpacksdcmdir command to convert my dicom files to mgz/nifti, and when i run the command: unpacksdcmdir -src DTI -targ DTI -scanonly DTI/scan.info I get an error message saying there are no dicom files found in the folder, whereas all of the dicom files for that sequence are in that folder (and when I use ls, all of the dcm files are listed). Can anyone help me as to why I am getting this error? Thanks, Caroline

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