Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Code changes to use Compiled Matlab?
by Bill Taylor 09 Aug '11

09 Aug '11

Mathworks loves their parallel toolbox. We love using Condor. I won't go into the reasons. http://www.cs.wisc.edu/condor/ We have negotiated an unlimited license of for Matlab and I have freesurfer recon-all broken into the three phases. This gives us currently 1700 dedicated cores where we can process brain scans for groups on the Madison, WI campus. We are contractually prevented from running anything but compiled Matlab on any cluster on the UW-Madison campus. I have had to modify "mris_computer_lgi" to call compiled matlab entry points after setting up a Matlab runtime within the Freesurfer 5.1.0 staged executable. What I ran into was a type mismatch from the way I now call the matlab functionality. Is there a known solution for this or do I have to change the matlab entry points to do initial type changing? We are working on a work flow to not only process the brains but also do FSL and matlab post processing at the same time and/or take preprocessed subjects and do either FSL or Matlab processing. I automate researchers on campus and don't actually program Matlab though I can work my way through this. As a computer Scientist I don't really want to be changing the code base in an unmanaged way. *********************************************************************Change in call # # make_outer_surface.m # # create the outer surface from the filled volume set MLF = /tmp/mos"_$$_".m set arg1 = ${tmpdir}/${input}.filled.mgz set arg2 = ${closespheresize} set arg3 = ${tmpdir}/${input}-outer rm -f ${arg3} # bt commented out for converting to compiled echo "Calling compiled matlab make_outer_surface" echo "make_outer_surface('${arg1}',${arg2},'${arg3}')" make_outer_surface ${arg1} ${arg2} ${arg3} #echo "make_outer_surface('${arg1}',${arg2},'${arg3}'); exit" > $MLF #echo "=================" #echo "`cat $MLF`" #echo "=================" #if ($RunIt) then #cat $MLF | ${MATLAB} -display iconic -nojvm -nosplash #endif ********************************************************************* ERROR BELOW Calling compiled matlab make_outer_surface reading filled volume... closing volume... ??? Error using ==> iptcheckinput Function STREL expected its second input, R, to be one of these types: double Instead its type was char. Error in ==> strel>ParseInputs at 1308 Error in ==> strel>strel.strel at 143 Error in ==> make_outer_surface at 41 ^G Images:strel:invalidType ********************************************************************* -- Bill Taylor 608-263-2656 (cell 608-219-4430) Center for High Throughput Computing(CHTC) Condor project Computer Sciences University of Wisconsin, Madison

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Modifying Regression Analysis
by Adam Nitenson 09 Aug '11

09 Aug '11

Hi Doug and Freesurfers, I am currently analyzing data acquired from the Sternberg memory task, which involves memorizing sets of 1, 3, 5, and 7 letters. I have created an analysis (see attached analysis.info and paradigm example) which allows me to create maps of the load-based activation when going from 1 to 3 to 5 to 7 letters, which accounts for the analysis' single "contrast". My PI was hoping that, for some subjects, we could look at the regression from JUST 1 to 3 to 5, since they have poor 7-letter data. >From looking at the analysis setup, it looks like I would have to make this change at the paradigm level since subjects have already been run with the current analysis with just the 1,3,5,7 regression contrast. I would probably have to change the "2"s in the paradigm file to "1"s for the 7-letter sets (since the contrast is 2vFix, and this alteration would essentially "ignore" the 7-letter condition), but a change at the paradigm file level, I believe, would essentially necessitate the formation of a new analysis entirely, which would then have to be run again individually on subjects, which can be a time consuming process. I was wondering if there was a way I could bypass this step and modify the analysis to suit these newer needs, or will I have to essentially make a new analysis based on my current one for this to work? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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Segmentation of hippocampal subfilelds
by mohan boddu 09 Aug '11

09 Aug '11

I have completed the segmentation of hippocampal subfileds, but now I would like to know the generated images are in probability map or label map? If they are in label map what would be the best upper and lower thresholds to generate the ROI mask images. Could you please also tell me the way to do so. -- --Mohan Boddu-- Research Assistant Department of Radiology and Imaging Research II Building Indiana University School Of Medicine Indiana University-Purdue University Indianapolis Indianapolis, IN 46202

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How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory?
by Sinem Burcu Erdoğan 09 Aug '11

09 Aug '11

Dear FreeSurfer Users; I am quite new to FreeSurfer and have just downloaded the full package. However; I do have a serious problem with introducing the license file to the system. The Freesurfer registration e-mail doesnot have any attachments but tells me to 'Place the three lines between the CUT HERE markers in a file named ".license" in the directory pointed to by the $FREESURFER_HOME environment variable' Am I supposed to cut and copy the three lines into the LICENSE file (I tried but was not allowed to make changes in it)? Or am I supposed to create a new file with an extension .license and copy it into the freesurfer folder? ( May seem irrelevant but I copied the LICENSE file to desktop; delete everything and put only the three lines between CUT HERE markers and saved the file with a .license extension and put it in the freesurfer directory- but it didnot help.) Your help is greatly appreciated. Thank you Here is your FreeSurfer license. Place the three lines between the CUT HERE markers in a file named ".license" in the directory pointed to by the $FREESURFER_HOME environment variable (see the FreeSurfer documentation). #---------------CUT HERE--------------- berdogan83(a)gmail.com 11403 *CQmdQSakwEaM #---------------CUT HERE--------------- The information you submitted was: title=Ms firstname=Sinem Burcu lastname=ERDOGAN institution_name=Bogazici University institution_type=nonprofit_education_research user_email=berdogan83(a)gmail.com address1=Bogazici Universitesi Biyomedikal Muh. Enstitusu Kandilli Kampus Cengelkoy address2=Kandilli Kampus rasathane cengelkoy city=Istanbul state=Uskudar zipcode=34684 country=turkey telephone=+905333965220 fax= OS/Platform=Darwin/Mac ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- Sinem Burcu ERDOĞAN Research Assistant Bogazici University Biomedical Engineering Institute Kandilli Kampüs 34684 Çengelköy / İSTANBUL TURKEY Tel :+90-216-5163433 Fax :+90-216-5163479 e-mail: burcu.erdogan(a)boun.edu.tr

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Using FreeSurfer with 6-14 year olds
by Felipe Picon 08 Aug '11

08 Aug '11

Dear FreeSurfer experts, I'm starting to recon-all the MPRAGE volumes of a large sample of 6-14 year olds So far I haven't had any errors (only 15 subjects runned so far) My questions are: - Should I make a template from the subjects of my whole sample, considering their age range? - Or FreeSurfer template would work just fine with this sample? If I should make a average from my whole sample, should I make it separating the sample in age ranges? Any suggestions are welcome Thank you!! -- *Felipe Picon, MD* Child and Adolescent Psychiatrist Master's Degree Student - Department of Psychiatry of Federal University of Rio Grande do Sul - UFRGS - www.ufrgs.br Adult ADHD outpatient research program - PRODAH-A - http://www6.ufrgs.br/prodah/prodah/equipe.html Hospital de Clinicas de Porto Alegre - HCPA - www.hcpa.ufrgs.br Member of the World Psychiatric Association (WPA) Early Career Psychiatrists Council Area Coordinator for the Americas - http://www.wpanet.org/detail.php?section_id=22&content_id=120 Web based CV: http://lattes.cnpq.br/3896757276389918 felipepicon(a)gmail.com

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kvlThresholdImage fails MacOSX 10.6.8
by Carl Anderson 08 Aug '11

08 Aug '11

Dear Freesurfer, I am using a 2 x 2.66 Ghz 6-Core Intel Xeon with 24Gb RAM and MacOSX 10.6.8 I tried running kvlThresholdImage from /subject/mri/ which resulted in the following error: ------------------ kvlThresholdImage orig.mgz /Applications/freesurfer/subjects/repeats/n10a/mri/orig/002.mgz X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 2 (X_ChangeWindowAttributes) Resource id in failed request: 0x2dc00ad0 Serial number of failed request: 7 Current serial number in output stream: 9 0 255 ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 542 vtkXOpenGLRenderWindow (0x31b8080): bad X server connection. DISPLAY=:0 Bus error _________ FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Kernel info: Darwin 10.8.0 x86_64 Thanks, -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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MCSRCH ERROR
by Irwin, William 08 Aug '11

08 Aug '11

Hi- I'm at a bit of a loss as to how to address and/or fix these errors. The native input images are very good quality; the conversion to T1.mgz is fine; the brainmask.mgz is good, a bit of dura remained at the parietal/occipital region (very common); otherwise, the skull stripping is very clean. The recon-all "finished" but with errors as expected. Processing "continued" to the end, but there is no output except in /mri and /touch. Doing: #@# Skull Stripping First under "Computing MAP estimate using 3481 samples..." IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10327.2 tol 0.000010 Then several of the same under "EM alignment process ..." IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 4 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 5 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 017: -log(p) = 1145822.4 tol 0.000000 Then again at "Computing MAP estimate using 2772 samples..." IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 7006.0 tol 0.000010 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 838978.4 tol 0.000000 Thanks, Wil ____________________________________ William Irwin | Brain Imaging Coordinator UCSF | Memory and Aging Center 350 Parnassus Avenue, Suite 905 San Francisco CA 94143-1207 wirwin(a)memory.ucsf.edu | memory.ucsf.edu p: 415.476.1680 | f: 415.476.1816

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Defining the Calcarine and distances from it in the Hinds et al. V1 label
by Krish Singh 08 Aug '11

08 Aug '11

Dear All, I've been trying out the automatic V1 labelling using the Hinds et al. (NeuroImage, 2008 vol. 39 (4) pp. 1585-99) and, as far as I can tell it seems to work pretty well on our anatomical scans (In general I'd be interested in the opinions/experiences of others who've tried it). I have a couple of questions: 1) Is it possible to automatically label just the calcarine itself? I know there is a pericalcarine label, but I am hoping to essentially label the line of the calcarine itself. 2) Is it possible to automatically find the occipital pole of the calcarine? The reason I want to do this is that it would then enable me to calculate the distance down the calcarine and the lateral distance away from the calcarine for each patch in the Hinds-V1 label. That potentially could be really useful in terms of sub-dividing the Hinds label into foveal and eccentric zones (although without retinotopy individual differences in M-scaling, for example, might limit interpretability). Would mris_divide_parcellation be useful here? Thanks in advance, Krish -- Prof. Krish Singh CUBRIC School of Psychology / Ysgol Seicoleg Cardiff University / Prifysgol Caerdydd Park Place / Plas y Parc Cardiff / Caerdydd CF10 3AT, UK Tel / Ffôn: 02920 874690 / 870365 Fax / Ffacs: 02920 870339 Email / Ebost : singhkd(a)cardiff.ac.uk

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freeview crash
by Hoptman, Matthew 08 Aug '11

08 Aug '11

Hi Ruopeg, No, glxgears doesn't crash. I'm getting about 3929 FPS. Thanks, Matt Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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FW: freeview crash
by Hoptman, Matthew 07 Aug '11

07 Aug '11

Hi all, I've been using Freesurfer for several years. I just upgraded to v. 5.1, but when I try to run freeview it crashes. I am running it on a 64-bit Centos 5.4 server and am accessing the server with Xming. When I try to start freeview it crashes Xming and I have to restart it. The only clue I have is when I try freeview.bin, I get "freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory". I'm wondering if it's a vtk problem. Any thoughts? --Matt Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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