Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

Re: [Freesurfer] localGI problems
by Marie Schaer 15 Jul '14

15 Jul '14

Hi Elisa, Thanks for the update, does that mean that just adding -f to all rm in load_mgh.m worked for you? Sounds great, thanks for keeping us posted! Indeed, it's not that nobody computed the lGI, lots of people used it in published studies and from what I see in the mailing list, and I definitely used it on tons of different computer configurations, and only in one case I got this error message. It was on a lab unix server shared between many people where the rm command was aliased to copy files to the recycle bin. Not having access to this rm parameters, even using the rm -f didn't solve the problem. So, it's definitely not an lGI issue, but a rm issue… Hope everything else will go well with your processing, Marie On Jul 3, 2014, at 2:59 AM, elisa veronese <dovreipensarci(a)gmail.com<mailto:dovreipensarci@gmail.com>> wrote: YEAH! Now it is working, the '-f' option is doing something! Actually it is still in progress, I do not know if it's going to work properly until the end. But at least something is happening :) Thank you, Marie! (Did you add the '-f' to all the rm in load_mgh.m?) Best, Elisa 2014-07-03 11:46 GMT+02:00 elisa veronese <dovreipensarci(a)gmail.com<mailto:dovreipensarci@gmail.com>>: Dear Marie, thank fot your email. I'm quite confused, it seems like nobody has ever computed this localGI :( Yes, before writing to the FS mailing list i checked in the internet if anybody had had my problem and I found your posts. I will try adding the -f to force the removal, it could be an idea. I'll let you know. Ehm... what do you mean by "to process the LGI on another computer"? Do you think it is a problem linked to the OS? Best, Elisa 2014-07-02 19:17 GMT+02:00 Marie Schaer <Marie.Schaer(a)unige.ch<mailto:Marie.Schaer@unige.ch>>: Hello Elisa, I've seen this issue that the process gets stuck even if you answer the question. That happened to me and others before, see the following posts: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg07251.html http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32912.html But I'm afraid that we didn't find the full solution to this yet. We tried replacing all the "rm" by "rm -f" in load_mgh.m, but it didnt help. Can you try that? Maybe you're more lucky than me. So finally, on my side, the only solution I found was to process the LGI on another computer… but it's definitely not ideal! Otherwise, maybe someone else has solved this issue without posting the reply on the mailing list. If yes, I'd be very grateful to know the answer, thanks in advance! Best, Marie On Jul 2, 2014, at 12:13 AM, elisa veronese <dovreipensarci(a)gmail.com<mailto:dovreipensarci@gmail.com>> wrote: Thank you Doug, anyway I'm afraid I still have problems with the recon-all -localGI. After answering yes to the removal of the temporary file, it seems that the program stops without doing anything. Now my tmp folder contains just one file (edit.dat). Below you can see what I see from my terminal. The terminal has been stuck there since yesterday. Thank you. Best elisa [root@gc02lx fselisa]# recon-all -s 1379341346/ -sd /root/Desktop/fselisa/ -localGI INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /root/Desktop/fselisa Actual FREESURFER_HOME /usr/local/freesurfer -rw-r--r--. 1 root root 1658172 Jul 1 17:30 /root/Desktop/fselisa/1379341346/scripts/recon-all.log Linux gc02lx 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /home/tmp/6004023.clrlcgce03.in2p3.fr/CREAM251988513/DIRAC_lhrUhWpilot/6418014/recon-all.sh-3038867747447129/freesurfer<http://6004023.clrlcgce03.in2p3.fr/CREAM251988513/DIRAC_lhrUhWpilot/6418014…> /root/Desktop/fselisa/1379341346/surf #-------------------------------------------- #@# Local Gyrification Index lh Tue Jul 1 17:31:13 CEST 2014 mris_compute_lgi --i lh.pial ================= rm -Rf /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2012 The MathWorks, Inc. R2012b (8.0.0.783) 64-bit (glnxa64) August 22, 2012 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com<http://www.mathworks.com/>. >> reading filled volume... rm: remove regular file `/tmp/tp1773697773286350.load_mgh.2127429.mgh'? y 2014-06-27 20:25 GMT+02:00 Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>>: #1. not a problem #2. yes, delete it doug On 06/27/2014 03:41 AM, elisa veronese wrote: > Dear FS users, > > I'm trying the -localGI on a linux Centos machine, but I'm facing some > problems: > 1. should I worry about the /Warning: Unable to open display > 'iconic'. You will not be able to display graphics on the screen. /?/ > / > 2. the script asks me if I wan to remove a file (rm: remove regular > file `/tmp/tp726715349117711.load_mgh.8128471.mgh'?). Should I say > yes and remove it? Is it important? Should I keep it? I tried > answering /no/, but now everything seems to be stuck without > performing any subsequent processing. > > Below there is the output I got. > > Thank you. > Regards, > elisa > > > [root@gc02lx fselisa]# recon-all -s 1379341346/ -sd > /root/Desktop/fselisa/ -localGI > INFO: FreeSurfer build stamps do not match > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is /root/Desktop/fselisa > Actual FREESURFER_HOME /usr/local/freesurfer > -rw-r--r--. 1 root root 1624545 Jun 26 18:08 > /root/Desktop/fselisa/1379341346/scripts/recon-all.log > Linux gc02lx 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT > 2013 x86_64 x86_64 x86_64 GNU/Linux > INFO: current FREESURFER_HOME does not match that of previous processing. > Current: /usr/local/freesurfer > Previous: > /home/tmp/6004023.clrlcgce03.in2p3.fr/CREAM251988513/DIRAC_lhrUhWpilot/6418014/recon-all.sh-3038867747447129/freesurfer<http://6004023.clrlcgce03.in2p3.fr/CREAM251988513/DIRAC_lhrUhWpilot/6418014…> > <http://6004023.clrlcgce03.in2p3.fr/CREAM251988513/DIRAC_lhrUhWpilot/6418014…> > /root/Desktop/fselisa/1379341346/surf > #-------------------------------------------- > #@# Local Gyrification Index lh Fri Jun 27 09:23:34 CEST 2014 > > mris_compute_lgi --i lh.pial > > ================= > rm -Rf /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial > ================= > ================= > mkdir -p > /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial > ================= > ================= > mris_fill -c -r 1 lh.pial > /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz > ================= > reading surface from lh.pial... > writing filled volume to > /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... > conforming output volume > setting resolution for intermediate calculations to 1.0000 > ================= > make_outer_surface('/root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); > exit > ================= > Warning: Unable to open display 'iconic'. You will not be able to > display graphics on the screen. > > < M A T L A B (R) > > Copyright 1984-2012 The MathWorks, Inc. > R2012b (8.0.0.783) 64-bit (glnxa64) > August 22, 2012 > > > To get started, type one of these: helpwin, helpdesk, or demo. > For product information, visit www.mathworks.com<http://www.mathworks.com/> > <http://www.mathworks.com<http://www.mathworks.com/>>. > > >> reading filled volume... > rm: remove regular file `/tmp/tp726715349117711.load_mgh.8128471.mgh'? > > > > -- > Elisa Veronese - PhD > > / > Research Unit on Brain Imaging and Neuropsychology (RUBIN) > / > / > Inter-University Center for Behavioral Neurosciences (ICBN) > University of Udine and University of Verona, Italy > / > ICBN Website: http://icbn.uniud.it/tiki-index.php > / > > / > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358<tel:617-724-2358> Fax: 617-726-7422<tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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. -- Elisa Veronese - PhD Research Unit on Brain Imaging and Neuropsychology (RUBIN) Inter-University Center for Behavioral Neurosciences (ICBN) University of Udine and University of Verona, Italy ICBN Website: http://icbn.uniud.it/tiki-index.php _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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<mailto:Freesurfer@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. -- Elisa Veronese - PhD Research Unit on Brain Imaging and Neuropsychology (RUBIN) Inter-University Center for Behavioral Neurosciences (ICBN) University of Udine and University of Verona, Italy ICBN Website: http://icbn.uniud.it/tiki-index.php -- Elisa Veronese - PhD Research Unit on Brain Imaging and Neuropsychology (RUBIN) Inter-University Center for Behavioral Neurosciences (ICBN) University of Udine and University of Verona, Italy ICBN Website: http://icbn.uniud.it/tiki-index.php

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Error in pre-processing in TRACULA
by 渡辺杏里 14 Jul '14

14 Jul '14

Dear TRACULA experts I am writing to ask about an error in pre-processing in TRACULA. After making FSL radiological header of dwi_orig_flip.nii.gz, an error occurs. When the name of file is changed from dwi_orig_flip.mghdti.bvals to bvals, I can't find the file dwi_orig_flip.mghdti.bvecs. So an error is mv: rename /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals: No such file or directory caused. The content of bvals is not overwritten. I attached my configuration file, the error log and bvals. Many thanks for your help. Best Wishes, Anri WATANABE -error log- fslorient -forceradiological /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz INFO: found /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvecs /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvecs mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals mv: rename /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals: No such file or directory ********************************************************************** 京都府立医科大学附属病院精神科・心療内科渡辺杏里 ********************************************************************** WATANABE ANRI Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine **********************************************************************

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label2MNI152 Transformation Help
by JacobML＠nmr.mgh.harvard.edu 14 Jul '14

14 Jul '14

Hello Freesurfer, I am attempting to take label files generated in fsaverage surface space and transform them into MNI152 volume space. Using the commands below, I am able to view the final output image with fslview in the the same space as the MNI brain. However, the registration is very off. Additionally, tkregister2 also displays the image in the same incorrect location. Any help identifying what may be going wrong with the registration/the transformation matrix would be greatly appreciated! Thank you for the help and or suggestions, Jacob 1. mri_label2vol --label M4_LH.label --subject fsaverage --temp /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/fsaverage/mri/orig.mgz --o M4_LH_orig.mgz --identity Terminal output: orig.mgz --identity INFO: subject not needed, igorning. Number of labels: 1 M4_LH.label Annot File: (null) Template Volume: /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/fsaverage/mri/orig.mgz Outut Volume: M4_LH_orig.mgz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: fsaverage Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; nlabels = 1 Allocating Hit Volume (16777216) voxels Loading M4_LH.label PVF (null) Thesholding hit volume. mri_label2vol done 2. mri_vol2vol --mov M4_LH_orig.mgz --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o M4_LH_orig_MNI152.nii.gz --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat Terminal output: Matrix from regfile: 0.998 -0.007 0.018 0.957; -0.013 -0.009 0.997 -17.816; -0.015 -1.001 0.002 -18.550; 0.000 0.000 0.000 1.000; movvol M4_LH_orig.mgz targvol /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz outvol M4_LH_orig_MNI152.nii.gz regfile /usr/local/freesurfer/stable5_3_0/average/mni152.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1406309355 Final tkRAS-to-tkRAS Matrix is: 0.998 -0.007 0.018 0.957; -0.013 -0.009 0.997 -17.816; -0.015 -1.001 0.002 -18.550; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: 1.995 0.035 0.015 33.682; -0.029 0.005 2.002 56.525; 0.026 -1.994 -0.019 218.527; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity INFO: writing registration to M4_LH_orig_MNI152.nii.gz.lta transformed matrix: 1.000 -0.000 -0.000 -1.000; -0.000 -0.000 -1.000 -17.000; -0.000 1.000 -0.000 19.000; 0.000 0.000 0.000 1.000; transformed matrix: 0.500 0.000 0.000 -18.500; 0.000 0.500 0.000 -9.500; 0.000 0.000 0.500 -18.500; 0.000 0.000 0.000 1.000; INFO: writing registration matrix to M4_LH_orig_MNI152.nii.gz.reg To check registration, run: tkregister2 --mov M4_LH_orig_MNI152.nii.gz --targ /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz --reg M4_LH_orig_MNI152.nii.gz.reg mri_vol2vol done 3. tkregister2 --mov M4_LH_orig_MNI152.nii.gz --targ /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz --reg M4_LH_orig_MNI152.nii.gz.reg Terminal output: tkregister_tcl /usr/local/freesurfer/stable5_3_0/tktools/tkregister2.tcl target volume /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz movable volume M4_LH_orig_MNI152.nii.gz reg file M4_LH_orig_MNI152.nii.gz.reg LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable M4_LH_orig_MNI152.nii.gz Tmov: -------------------- -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 -1.000 0.000 0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = fsaverage Zoom Factor = 2, SQR() = 4 FOV = 256 Opening window fsaverage Opening fsaverage, xnum = 256, xdim = 512 Setting scale tkregister2: interface: /usr/local/freesurfer/stable5_3_0/tktools/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change: macro,mini,micro) tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}

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holes in inflated using mris_label2annot
by April Clausen 14 Jul '14

14 Jul '14

When viewed on the inflated surface in tksurfer, we are seeing “holes” in annot files we created defining our own ROIs. We first created 6 label files on fsaverage then mapped these 6 label files to 5 different subjects using mri_label2label. Once the 6 label files were mapped to each subject, we used mris_label2annot to create an annot from the 6 labels for each subject. This process all seemed to run without errors. We then used tksurfer to view the annot file on the inflated surface for each subject. “holes” appeared in 1-2 of the regions defined by the label files for each subject. We are concerned that these “holes” imply that not all the surface is being included in the region which will in turn result in not all surface being included in the stats files created with the kris_anatomical_stats program.

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recon-all for kids
by Alshikho, Mohamad J. 14 Jul '14

14 Jul '14

Hi Fs Expert, I have a group of kids subjects (4-15) year old. I want to do cortical reconstruction process using Freesurfer. My question is: is still correct to use the command line <recon-all -all -subjid> in this age group? Do I need to use the flag -noseg ? (i.e can I use aseg for this range of age) Thanks, Mohamad

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Re: [Freesurfer] Fw: Aw: Re: Problem with uploading Cluster Simulation data
by Douglas N Greve 14 Jul '14

14 Jul '14

what is your command line? Or otherwise, how are you visualizing it? On 07/14/2014 08:09 AM, carina(a)van-vlodrop.de wrote: > *Gesendet:* Sonntag, 06. Juli 2014 um 22:48 Uhr > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > *An:* "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > *Betreff:* Aw: Re: [Freesurfer] Fw: Problem with uploading Cluster > Simulation data > Hi Doug, > I have already uploaded a text file of my corrected results from the > Monte Carlo Cluster Simulation which reports 15 Clusters (attached > picture). > There is another file ending with .mgh and the tutorial identifies it > to be the overlay (clusterwise corrected map) which I can upload in > freeview. > In freeview there are the alternatives of uploading a surface or a > volume. If I upload the file ending with .mgh as a volume I just > recieve a black image with a few numbers on the coordinate plane > (attached picture). There is no brain visible. > Is it correct to upload the overlay (file ending with .mgh) as a > volume or how should I proceed? Do I have to upload a template first > and which is the right template? > Thank you so much. > Yours sincerely, > Carina > *Gesendet:* Montag, 16. Juni 2014 um 12:45 Uhr > *Von:* "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> > *An:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de>, "free surfer" > <freesurfer(a)nmr.mgh.harvard.edu> > *Betreff:* Re: [Freesurfer] Fw: Problem with uploading Cluster > Simulation data > > You should be able to view the map results in freeview just as you > would any other map. > doug > > > > > > On 6/12/14 12:19 PM, carina(a)van-vlodrop.de wrote: > > *Gesendet:* Dienstag, 10. Juni 2014 um 11:18 Uhr > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > *An:* freesurfer(a)nmr.mgh.harvard.edu > *Betreff:* Problem with uploading Cluster Simulation data > Dear freesurfer experts, > we are conducting cortical-thickness analysis using > freesurfer-4.4.0 and the final analysis with qdec. I have a > question concerning the Clusterwise Correction for Multiple > Comparison. > Is it correct that I have to visualize the results of the Monte > Carlo Simulation in freeview? > Do I have to upload a special model in freeview before uploading > the Cluster Simulation data? > Yours sincerely, > Carina > > > _______________________________________________ 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Question about LGI
by pfotiad＠nmr.mgh.harvard.edu 14 Jul '14

14 Jul '14

Hi FS Community, I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume. Thanks in advance, Panos

5 10

trac-all -prep error field map error
by Eileen Moore 14 Jul '14

14 Jul '14

Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring to run tracula on some images acquired from a GE scanner. I am running into problems when I try to perform the registration-based B0-inhomogeneity compensation, getting an error in the terminal output: "ERROR: Unrecognized format of phase map". However, trac-all -prep runs fine when I skip the B0-inhomogeneity compensation step. Is there something else I need to do to use field map correction? I've attached the trac-all.log and a copy of the terminal output. Thanks, Eileen.

2 1

LME Longitudinal QDEC Table
by Elijah Mak 14 Jul '14

14 Jul '14

Hello Freesurfer Experts, I am performing a mass-univariate analyses using the LME toolbox for longitudinal studies. After running both mris_preproc and mri_surf2surf , I load the lh.thickness_sm10.mgh file using *[Y,mri] = fs_read_Y('lh.thickness_sm10.mgh');* Next, I run the following command: *Qdec = fReadQdec('qdec.table.dat');* However, it seems that the output is entirely in string format "166 x 1 cell". The first row reads as "'fsid fsid-base years group gender age'" in a single column. Because of this, I am running into problems when I try to execute the following steps: *Qdec = rmQdecCol(Qdec,1);* (removes first column) *sID = Qdec(2:end,1); (grabs the subjects' IDs)* *Qdec = rmQdecCol(Qdec,1);* (removes the subjects'ID column) *M = Qdec2num(Qdec);* (converts to a numeric matrix) *[M,Y,ni] = sortData(M,1,Y,sID);* (sorts the data) Your help will be greatly appreciated! Many thanks. Best Regards, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

2 5

Re: [Freesurfer] Patch that adds parapool support to lme_mass_F, lme_mass_fit_EMinit, lme_mass_fit, lme_mass_fit_init. lme_mass_fit_Rgw
by jorge luis 14 Jul '14

14 Jul '14

Hi Knut Thank you very much for your contribution. I'll take a look at it and apply the patches as soon as I have time (probably next weekend) on github: https://github.com/NeuroStats Best -Jorge >________________________________ > De: Knut J Bjuland <knut.j.bjuland(a)ntnu.no> >Para: jorge luis <jbernal0019(a)yahoo.es> >Enviado: Jueves 26 de junio de 2014 5:16 >Asunto: Patch that adds parapool support to lme_mass_F,lme_mass_fit_EMinit, lme_mass_fit,lme_mass_fit_init. lme_mass_fit_Rgw > > >Dear Dr Rusiel > >Matlabpool is deprecated in Matlab 2014a. I have therefore written a >patch, which adds parapool support when Matlab 2013B and above is used >vertex wise linear mixed model is used. >Please review the patch? Is the patch sound? Please apply the patch. > >Your sincerly > >Knut J Bjuland > > > >

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Freesurfer July 2014