Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

Re: [Freesurfer] installation problem in ubuntu
by Pedro Paulo de Magalhães Oliveira Junior 23 Feb '11

23 Feb '11

try the command: sudo apt-get install tcl -- PPJ Please: cc the freesurfer list when answering 2011/2/22 Carolina Valencia <cvalencia(a)linkdx.com.co> > Hi Pedro, > > Finally, I could install it with the license file and the environment is > properly set without warnings. > But trying to test it, following the instruction on the wiki page I have a > problem > > cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit bert orig.mgz > /usr/local/freesurfer/bin/tcl_setup: No existe el fichero o el directorio. > > in the .bashrc I copy the right location of the freesurfer folder > FREESURFER_HOME=/home/cvalencia/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > > 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > >> run this command >> >> sudo rm -rf $FREESURFER_HOME >> >> >> >> 2011/2/21 Carolina Valencia <cvalencia(a)linkdx.com.co> >> >>> Thanks Pedro, >>> >>> How I uninstall that version to re-install the correct version? >>> I look for some answers and try >>> >>> rm -rf $FREESURFER_HOME >>> >>> It says that I don't have permission,how I can unistall it, if i'm the >>> admin user? >>> >>> Thanks in advance, >>> >>> Carolina >>> >>> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br >>> > >>> >>>> It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS >>>> >>>> >>>> 2011/2/21 Carolina Valencia <cvalencia(a)linkdx.com.co> >>>> >>>> >>>>> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae >>>>> #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux >>>>> >>>>> Thanks, >>>>> >>>>> >>>>> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior < >>>>> ppj(a)netfilter.com.br> >>>>> >>>>> Please send the result of the command: >>>>>> >>>>>> uname -a >>>>>> >>>>>> >>>>>> On Mon, Feb 21, 2011 at 10:31, Carolina Valencia < >>>>>> cvalencia(a)linkdx.com.co> wrote: >>>>>> >>>>>>> Hi Bruce, >>>>>>> >>>>>>> I'm experimenting problems with the installation on Ubuntu too. >>>>>>> There's is warning in the welcome message, it seems that something is >>>>>>> missing: >>>>>>> >>>>>>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 -------- >>>>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>>>>>> WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist >>>>>>> FREESURFER_HOME /home/cvalencia/Descargas/freesurfer >>>>>>> FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast >>>>>>> FSF_OUTPUT_FORMAT nii >>>>>>> SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects >>>>>>> MNI_DIR /home/cvalencia/Descargas/freesurfer/mni >>>>>>> FSL_DIR /usr/share/fsl/4.1 >>>>>>> >>>>>>> >>>>>>> I try to test it and it shows >>>>>>> cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit >>>>>>> /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de >>>>>>> ejecutable incorrecto. Binary file not executable. >>>>>>> >>>>>>> Thanks a lot, >>>>>>> >>>>>>> Carolina >>>>>>> >>>>>>> 2011/2/18 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>>>>>> >>>>>>>> Hi Jie, >>>>>>>> >>>>>>>> what hardware are you using? Is it a 64 bit operating system? >>>>>>>> >>>>>>>> cheers >>>>>>>> Bruce >>>>>>>> >>>>>>>> On Sat, 19 Feb 2011, Liukarl wrote: >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Hello, Freesurfer experts: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> I am new to freesurfer and try to >>>>>>>>> install the newest version of freesurfer in Ubuntu system. I >>>>>>>>> closely >>>>>>>>> followed the instructions, and the only difference is that I >>>>>>>>> installed it in my Documents, instead of local folder. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Below is the output after “source >>>>>>>>> $FREESURFER_HOME/SetUpFreeSurfer.sh” >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -------- >>>>>>>>> freesurfer-Linux-centos4-stable-pub-v5.0.0 -------- >>>>>>>>> >>>>>>>>> Setting up environment for >>>>>>>>> FreeSurfer/FS-FAST (and FSL) >>>>>>>>> >>>>>>>>> FREESURFER_HOME >>>>>>>>> /home/jie/Documents/freesurfer/ >>>>>>>>> >>>>>>>>> FSFAST_HOME >>>>>>>>> /home/jie/Documents/freesurfer//fsfast >>>>>>>>> >>>>>>>>> FSF_OUTPUT_FORMAT nii >>>>>>>>> >>>>>>>>> SUBJECTS_DIR >>>>>>>>> /home/jie/Documents/freesurfer//subjects >>>>>>>>> >>>>>>>>> MNI_DIR >>>>>>>>> /home/jie/Documents/freesurfer//mni >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Everything seems fine and I also added >>>>>>>>> the .license file to the freesurfer folder. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> But when I test it by “tkmedit bert >>>>>>>>> orig.mgz”, it reponds “Illegal instruction” >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> If I type in “recon-all”, it will >>>>>>>>> show >>>>>>>>> >>>>>>>>> “ Required Arguments: >>>>>>>>> >>>>>>>>> -subjid <subjid> >>>>>>>>> >>>>>>>>> -<process directive>…... >>>>>>>>> ” >>>>>>>>> and the other arguments. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> How to fix the problem and make >>>>>>>>> Fressurfer run? Any help is appreciated. Thanks a lot! >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Jie >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>> whom it is >>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>> the e-mail >>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>> HelpLine at >>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>> you in error >>>>>>>> but does not contain patient information, please contact the sender >>>>>>>> and properly >>>>>>>> dispose of the e-mail. >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the person to >>>>>>> whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>> the e-mail >>>>>>> contains patient information, please contact the Partners Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>> you in error >>>>>>> but does not contain patient information, please contact the sender >>>>>>> and properly >>>>>>> dispose of the e-mail. >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>> >>> >>> >>> -- >>> >> >> > > > -- >

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ASL tag-control order
by Rita Loiotile 23 Feb '11

23 Feb '11

Hi, How can I tell what the tag-control order of collection was for my ASL images? They were all acquired in Bay 3. I can get you other parameters if you need...

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question about qdec analysis
by 汪贵宏 23 Feb '11

23 Feb '11

Hi everybody, I am new user of Freesurfer,I simply take five procedures to process my data ,after I read the wiki on the website. The five procedures including: 1. mri_convert one-dicom-file-from-series blobby.nii.gz 2.recon-all -i blobby.nii.gz -subjid blobby –all 3.recon-all -s <subjid> -qcache 4.make_average_subject. 5.qdec Now, my questions are: 1.In our e-mail ,you often talk about recon-all, why did I never across question about it ? 2. I tried to run the qdec-tool, but experienced some problems . I got different thickness in one area. In detail: 1. When I open theqdec.table.dat ,the thickness is different from the thickness got from the display in Find Clusters and Goto Max, I really do not know why? 2. Did I get the same results from two differentqdec.table.dat , one qdec.table.dat has 34 Continuous Variables but the other had only one Continuous Variable ? 3.Why did the display from qdec smaller than the examples in the wiki on the website? Such as the pictures follow. I guess part of my problem is that I'm having trouble understanding exactly how to use the freesurfer. Can you try to give me a sort of layman's explanation? Thanks for your answer! wang

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TKSurfer question
by Weisinger, Brian (NIH/NIMH) [F] 23 Feb '11

23 Feb '11

Is there a way to get a general generic TK_Surfer output without using a subject? Thanks, Brian Weisinger

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Help ! Error for generating *.mgz files
by xiaotian yin 23 Feb '11

23 Feb '11

Dear Bruce, Thank you so much for taking care of my stupid questions :) I searched online regarding the ANALYZE vs Dicom, and I understand your point now ... The problem is, for this scan, I am afraid the only data format that I can play with is ANALYZE ... (although there might be Dicom format available on later scans) So ... I tried some other tools and got the orientation information out of the ANALYZE data (not sure if it makes sense ...) 0.7000 0 0 0 0 0.7000 0 0 0 0 1.5000 0 0 0 0 1.0000 I save them in a *.mat file, and seems that mri_convert did the job successfully, I got the *.mgz file. Then I setup the necessary directories ( i.e. my_new_subjects_dir/subj001/mri/orig ), put the *.mgz file there, and launched " recon-all -all -s subj001 ". Then I got some warnings and errors (see below), and here comes my new questions, if you do not mind ... ** Question-1 : After launching recon-all, got a warning immediately (see below). Sorry for my stupid questions ... but what is a typical input I should feed to recon-all ? Two scans of the same whole brain? Or one scan for the left hemisphere scan and another one for the right hemisphere? Or something else ? "WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue." ** Question-2 : The program seems running well after the warning, until it terminates a couple of minutes later, throwing out some error like below. I just have no idea what to do now ... Could you please give me some hints? "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)" The complete output from recon-all is attached, for your information. If you need the data, is there any way I can send it to you without bothering other members in the mailing list? Thank you ! Best Regards Tim On Sun, Feb 20, 2011 at 9:47 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Tim, > > it doesn't help to convert from analyze to something else. Once you have > gone through analyze all direction information is lost. Can you get access > to the data before it was converted to analyze in whatever format the > scanner produced? > Bruce > > On Sun, 20 Feb 2011, xiaotian yin wrote: > >> Dear Bruce, >> >> >> THanks for the quick response! >> >> I searched online for Analyze --> Dicom converter ... no luck ... >> >> Also tried to read the Analyze file (*.hdr) into Matlab, ending up >> with the following info : >> >> Filename: 'IA_1_orig.hdr' >> FileModDate: '04-ÿÿÿÿ-2010 01:08:20' >> HdrFileSize: 348 >> ImgFileSize: 8126464 >> Format: 'Analyze' >> FormatVersion: '7.5' >> Width: 256 >> Height: 256 >> BitDepth: 8 >> ColorType: 'grayscale' >> ByteOrder: 'ieee-le' >> HdrDataType: 'volume ' >> DatabaseName: 'IA_1_%%%.pic.' >> Extents: 16384 >> SessionError: -28067 >> Regular: 1 >> Dimensions: [256 256 124 1 1] >> VoxelUnits: '' >> CalibrationUnits: 'Y??·2w?·' >> ImgDataType: 'DT_UNSIGNED_CHAR' >> PixelDimensions: [1x5 single] >> VoxelOffset: 0 >> CalibrationMax: 255 >> CalibrationMin: 0 >> Compressed: -2.7107e-005 >> Verified: -2.7172e-005 >> GlobalMax: 255 >> GlobalMin: 0 >> Descriptor: [1x80 char] >> AuxFile: '?J?· ?ù·? ?oü·????°???' >> Orientation: 'Orientation unavailable' >> Originator: ' ·???' >> Generated: ' p' >> Scannumber: '??· ' >> PatientID: '' >> ExposureDate: '' >> ExposureTime: '' >> Views: 0 >> VolumesAdded: 0 >> StartField: -1209816480 >> FieldSkip: -1208305456 >> OMax: -1208193036 >> OMin: -1208460092 >> SMax: -1208306728 >> SMin: -1077308224 >> >> >> >> Did not see any "hist.orient" field or affine transformation field ... >> >> Do you have any recommendations ? >> >> >> Best >> Tim >> >> >> >> >> On Sat, Feb 19, 2011 at 9:46 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>> Hi Tim, >>> >>> the .hdr/.img format is called Analyze, and it doesn't come with >>> orientation informaton. This means that it is easy for example to get a >>> left/right swap that you will never know was in your data. Can you get it >>> in any other format, like dicom, or whatever format it came off the >>> scanner >>> in? >>> >>> If not, you can send us one of the pairs of files that gives the segfault >>> and we'll take a look >>> >>> cheers >>> Bruce >>> >>> >>> >>> On Sat, 19 Feb 2011, xiaotian yin wrote: >>> >>>> Hi, >>>> >>>> Thank you for reading this email ! >>>> >>>> I am a newbie to Medical Imaging, and am learning to use FreeSurfer >>>> for surface construction. >>>> >>>> Already installed FreeSurfer in Ubuntu, and the installation has been >>>> verified to be 100% successful. >>>> >>>> I got a bunch of data (coming in pairs of *.hdr and *.img), and I am >>>> trying to convert them to *.mgz files, so that I can use recon-all >>>> then. >>>> >>>> but when I call mri_convert as follows: >>>> >>>> mri_convert Rcing.img Rcing.mgz >>>> >>>> I got the following error : >>>> >>>> >>>> mri_convert Rcing.img Rcing.mgz >>>> $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ >>>> reading from Rcing.img... >>>> ----------------------------------------------------------------- >>>> INFO: could not find /mnt/Data/Rcing.mat file for direction cosine info. >>>> INFO: use Analyze 7.5 hdr->hist.orient value: -40, . >>>> INFO: if not valid, please provide the information in >>>> /mnt/Data/Rcing.mat file >>>> ----------------------------------------------------------------- >>>> Segmentation fault >>>> >>>> >>>> I have searched the freesurfer website ... no luck .... >>>> Would you mind to give me some advice or hints ? Thank you so much ! >>>> >>>> >>>> Best >>>> Tim >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> >> >

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Neuroimaging Data Processing Workshop 23-24 March 2011, Edinburgh, UK
by Chris Filo Gorgolewski 23 Feb '11

23 Feb '11

Dear all, I am delighted to invite you to a Neuroimaging Data Processing Workshop which will be held on 23-24th of March 2011 at University of Edinburgh, UK. During the workshop we will cover neuroimaging data analysis and management with reusable, scalable and reproducible processing workflows that combine different software packages (such as SPM, FSL, and FreeSurfer) using NiPyPE framework. The workshop will also feature talks and demos covering data management, encapsulation and visualization using PyXNAT and the Connectome Library and Viewer. More details can be found at the workshop website: http://nipype.blogspot.com Best regards, Chris Gorgolewski

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longitudinal analysis
by nadia merhoum 23 Feb '11

23 Feb '11

Hello I have just started to use FreeSurfer (version 4.5) and have some questions on the longitudinal stream: I have started to process cross-sectionally all time points (7 tp) of my patients with the following script: recon-all –i tpidN.nii –subjid tpidN* –all* Then, created an unbiased template from all time points for each subject and process it with recon-all with the following script: recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all and finally did the longitudinal process to all time points with the following script: recon-all -long <tpNid> <templateid> -all I would like to know if what I have been doing till this final step is correct or not? I would like also to know how we could calculate the differences between tpid1.long.template and tpid2.long.template for example? And is there any automatic way to do so? Thank you for your help Sincerely Nadia

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mkanalysis-sess says ERROR: bad format for seq.info file
by Pablo Polosecki 23 Feb '11

23 Feb '11

Hi all, I am trying to define an analysis for a block-based functional scan using mkanalysis-sess. When I run it, I get the following output with an error message: Setting TER to .10000000000000000000 /home/ppolosecki/space/data/ppolosecki/cooked/2011/110211Quincy ERROR: bad format for seq.info file, /home/ppolosecki/space/data/ppolosecki/cooked/2011/110211Quincy The seq.info file (attached) was produced by the unpacksdcmdir command and it looks no different from other ones I have seen. The information there seems correct to me. Could someone perhaps point out possible reasons why this could happen? The script I use to call mkanalysis-sess containing all the parameters used is attached. Thank you in advance. Pablo -- Pablo Polosecki Graduate Fellow Laboratory of Neural Systems The Rockefeller University 1230 York Avenue, Box 9 New York, NY 10065 Tel: 212-327-7699 (Lab) 917-842-2510 (Cell) email: ppolosecki(a)mail.rockefeller.edu

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recon-all on data with anatomical abnormality or strong artifact
by Eveline Geiser 22 Feb '11

22 Feb '11

Hi, I run into the following error when running recon-all. ERROR: _FindFacePath: could not find path! in the process: Correcting Topology of defect 2 with euler number -9 (5 loops) computing statistics for defect 2: 1934 vertices location: [ (93,119,57) - average intensity = 85.136 ].... The subject also has a huge anatomical abnormality or possibly an artifact ventral of the cerebellum (between cerebellum and pons). Brainmask.mgz also shows striping. When running the old topology fixer the following error occurs: mris_fix_topology: could not read brain volume from /mindhive/gablab/rhythm/cacophonix_July10/freesurfer_data/cacix7/mri/brain however, brain.mgz is there and loadable in tkmedit. Could the artifact be the reason for all this or is there another issue? Thanks for your help Eveline -- --------------------- Eveline Geiser PhD Massachusetts Institute of Technology Department of Brain and Cognitive Sciences phone: +617 324 63 71 e-mail: egeiser(a)mit.edu http://web.mit.edu/gabrieli-lab/

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question about weighted regression analysis
by Katie Bettencourt 22 Feb '11

22 Feb '11

So I created a weighted regression analysis to look at the effect of memory load in a particular brain region. Basically, I weighted the paradigms by a behavioral measure that reflected the number of items actually remembered (as set size was increased). As far as Doug told me there are basically 2 ways to weight your paradigm files. Version 1: Have 2 conditions, baseline (condition 0) and all the set sizes (condition 1). Condition 1 would then be weighted by the behavioral measure. Version 2: Have 3 conditions, baseline (condition 0), and then I represented each presentation as two different conditions, one with a weight that is always 1 (condition 1), the other weighted according to the behavioral measure (condition 2). The difference, as far as I understand it, in version 1, it is assumed that the response amplitude is ) when the weight is 0 (ie. that when you are attending to 0 items, brain activity = 0). Whereas, version 2, tests the slope of the HRF amplitude vs weight without the assumption above. However, I'm a bit confused as to the results I got. When I looked at the data from both versions, version 1 provided a much higher amount of activation and more areas activated than version 2. However, I believe version 2 better fits with the multiple regression analysis that is done in Brain Voyager. Can anyone give me a better explanation of what the difference between these analysis models is? Katie

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Freesurfer February 2011