Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Registration and Surafce Flattening
by Caka 28 May '14

28 May '14

Hi Bruce, Yes I am trying to do some quantitative analysis rather than just displaying the patches. The only way I know for getting the vertex indices and the coordinations is reading it into matlab. (1) flat = read_patch(‘lh.cortex.patch.flat’); This command worked today! I rebooted my system. (2) patch = read_asc(‘lh.cortex.patch.flat.asc’); This command still couldn’t work. The error information is: ??? Error using ==> reshape To RESHAPE the number of elements must not change. Error in ==> read_asc at 39 v = reshape(v, [4 S(2)])’ ; Thanks very much! Qiongmin --------------------- Original email ----------------------- Hi Qiongmin why are you trying to read the patches into matlab? Also, can you send us your full matlab command that generated the error? Sounds like you passed the incorrect file name cheers Bruce On Tue, 27 May 2014, Caka wrote: > Thank you Bruce, > > I convert the fsaverage flat map into a ascii file, using: ? mris_convert > ?-p ?lh.cortex.patch.flat ?lh.cortex.patch.flat.asc. > Now I need to read these two files. > > (1) I used read_patch.m to read lh.cortex.patch.flat. But an error came out, > it said ? Error using ==> read_patch at 28, could not open file ??. > (2) I couldn?t find a read_patch_asc.m script in Freesurfer, as is suggestedin?https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/m… > tml > (3) I found a read_asc.m instead, but when I used it to read the > lh.cortex.patch.flat.asc, an error occurred: ?Error using ==> fgets, > ?Invalid file identifier. Use open to generate a valid file identifier?. > > Could you please give me some advices?Thank you very much! > > Best regards, > Qiongmin > > > ????????????????Original email--------------------------------------- > Hi Qiongmin > > 1. I think this is a bug in the open GL code that is outside of our? > control. We will try to track it down > > 2. The flat maps aren't really any different than say the inflated? > fsaverage surface. If you can generate group (or individual maps) in? > fsaverage space you can display them on the flat maps. > > 3. The index of each vertex in the flattened space is stored in the patch? > files so you can always look up what vertex it was on inflated, sphere,? > etc... > > cheers > Bruce > > > On Mon, 26 May 2014, Caka? > wrote: > > Dear Bruce, Doug and all, > Thanks for your suggestion, it helped a lot. > > (1) I load the fsaverage surface (lh.inflated) in tksurfer, and > then load > the fsaverage patch (lh.cortex.patch.flat). The flat map was > shown for > several seconds, and then ?an error occurred and tksurfer was > shut down. The > terminal said: ?tksurfer.bin:tnl/t_vertex.c:407: > update_input_ptrs: > Assertion ?a[j].inputstride == vptr-> stride? failed. Abort(core > dumped)?. > ?Could you give me some advice? > I use a 'CentOS release 6.2' system. The freesurfer is > ?freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0?.? > > (2) Indeed, I want to flatten all cortical thickness surfaces of > 140 > subjects onto the ?lh.cortex.patch.flat? of fsaverage. I just > don?t > understand your idea how to do this. After I load > ?lh.cortex.patch.flat? of > fsaverage, the tksurfer only shows this flat map (now it lasted > for several > seconds and crashed), so how can I ' load whatever overlay you > want in the > same way you would on the inflated surface?? > Does it mean that I load the individual flat map on the > individual inflated > surface? But I haven?t got the individual flat map yet.? > > (3) I am wondering if there are some table recording the > transformation > relationships between the fsaverage surface vertices and the > flat map > vertices? If so, then I think all I need to do is extracting the > cortical > thickness value of every vertex in individual inflated surface, > and then > putting into the corresponding vertex in the flat map.? > > Thank you very much!? > > Best regards, > Qiongmin? > > >

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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

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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

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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

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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

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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

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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

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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

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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>

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