Re: [Freesurfer] retinotopic mapping selxavg3-sess error
Sorry for the delay. I'm new to FSL, Freesurfer, and VB, so maybe I'm doing it wrong, but I have the impression I cannot run FSL from the VB: - Typing 'fsl' yields 'fsl: Command not found'. - Checking the environment with 'echo $FSLDIR' yields 'FSLDIR: undefined variable' - Checking the path with 'flirt -version' yields 'flirt: Command not found' However, typing 'fsl' + tab shows the following available commands: - fsl2par - fsl_label2voxel - fslmaths.fsl - fslorient.fsl - fslregister - fslregister -sess - fsl_rigid_register - fslsfonts - fsl_sub_seychelles - fslswapdim.fsl So it seems there are some FSL-related files installed, but apparently not all. I did download the virtual disk image for Freesurfer, so I assumed a complete FSL version would be included? I'm sorry if there's an obvious solution, but I can't seem to find it... Thanks again, Bianca On Fri, Jun 21, 2013 at 6:16 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: Can you run FSL at all in your VB? On 6/21/13 7:49 AM, Bianca van Kemenade wrote: Dear Freesurfers, I'm setting up freesurfer to do retinotopic mapping. I use a PC with Windows XP, so I installed Freesurfer using the VirtualBox (with Xubuntu). I managed to get through the initial steps for retinotopic mapping, but I get stuck at the actual analysis. The point where I get stuck is: selxavg3-sess -a rtopy.self.lh -s P2_BK It starts the analysis, but runs into problems at the stage Using FSL's BET to extract brain and gives the following error output: # -- Using FSL's BET to Extract Brain-- # /home/virtualuser/freesurfer/ shared/P2_BK/bold bet.fsl /tmp/mkbrainmask_4425/in.nii /tmp/mkbrainmask_4425/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found /bin/rm: cannot remove `_tmp*': Protocol error ERROR: bet failed I tried updating FSL in case that is the problem, but it is only available for Ubuntu 10.04 and up, whereas the Ubuntu system that is provided to install the Freesurfer virtual disk image is 9.04. If anyone has an idea how to proceed let me know, any help is much appreciated. Thanks, Bianca ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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. -- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/ -- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/ ___ Freesurfer mailing list 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] Error for mri_glmfit contrast
Dear Freesurfer experts, I am currently trying to do a cortical thickness group analysis with one factor, three levels . I have run mri_preproc and mri_surf2surf, and am now trying to run mri_glmfit --y lh.group.thickness.10B.mgh --fsgd easy2.file --C contrast1.mtx --surf fsaverage lh --cortex --glmdir lh.group However, I keep getting this error; INFO: gd2mtx_method is doss Saving design matrix to lh.group/Xg.dat Normalized matrix condition is 1 Matrix condition is 7 Found 149955 points in label. Pruning voxels by thr: 0.00 Found 149953 voxels in mask Saving mask to lh.group/mask.mgh Reshaping mriglm-mask... search space = 74612.446501 MatrixReadTxT: could not scan value [2][1] The format of both the fsgd file and the contrast file is ASCII text My fsgd file is formatted as follows: GroupDescriptorFile 1 Title Group analysis Class HR Class Con Class ILL Input EHRS__2 HR Input EHRS__2 HR Input EHRS__2 HR Input EHRS__2 Con Input EHRS__2 Con Input EHRS__2 ILL and my contrast file is; 1 -1 0 I do not understand why I keep getting this error. When I include the flag -no-contrasts-is-ok, the mri_glmfit does work. There are no commas in either file. This leads me to believe something is wrong with my contrast file? However I am not certain what this could be. Help would be greatly appreciated. Thank you very much, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ Freesurfer mailing list 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] problem with surface area regression
Dear Freesurfer, I have checked the mail list, none could answer my problem. I added up the value of all vertxes in the .area or .area.pial files, find that brain size did not contribute much to that vertex-sum. However, some experiment used total brain volume as a regreesion coefficient to remove brain size effect. In these case, with the comparison of surface area in vertex-to-vertex, is it proper to use the above vertex-sum as the regression coefficient to remove different brain size? Thank you very much! Cowen 2013-06-24 wen.zhang55 ___ Freesurfer mailing list 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.
Re: [Freesurfer] lme issues + failure to converge
Hi Cathy If you only have three groups in your data (Control subjects, High risk patients, Ill patients) then you should drop the “Controls versus all others and controls*time interaction” terms from your design matrix. Otherwise it is ill-conditioned. One way to check your design matrix is by performing a simple univariate analysis using data from a single vertex, eg. at vertex 1000: lhstats = lme_fit_FS(X,[1 2],Y(:,lhcortex(1000)),ni); and check the behavior of the optimization procedure. Make sure that both your design matrix X and the cortical thickness data Y are ordered in a way that they contain all the repeated measures for the first subject (ordered by time), then all the repeated measures for the second subject and so on. The first element of the vector ni must indicate the number of repeated measures in the design matrix X for the first subject, the second element of that vector must indicate the number of repeated measures in the design matrix for the second subject and so on. Finally you should include the data Y as an argument of the fitting function: lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex); This will fit a linear mixed effects model with two random effects (intercept and time). Best -Jorge De: Catherine Bois c.b...@sms.ed.ac.uk Para: Jorge jbernal0...@yahoo.es CC: freesurfer@nmr.mgh.harvard.edu Enviado: Lunes 24 de junio de 2013 5:14 Asunto: Re: [Freesurfer] lme issues + failure to converge Hi, So, the model we fitted was one with only 1 random effect apparently (the intercept term), so we used the script you sent for older versions of matlab; lhstats = lme_mass_fit_vw1(X,[1],ni,lhcortex) The model took 861 minutes to run, and at the end it now said that the model failed to converge at ca 85% of locations... The matrices columns are as follows; the intercept term, time (I guess due to only using one random effect in our model it will be treated as a fixed effect by Matlab?), High risk versus all other patients, high risk versus time interaction, Controls versus all others, controls*time interaction, ill*all others, ill*time interaction, Gender, Age. There are ca 170 subjects, with varying and unbalanced repeated measures (ranging up to 5/subject). Since we would like to fit a model with both intercept and time (and in the long run) also family as random effects, perhaps we need to use the spatiotemporal models instead to make our model converge? If so, will the scripts for fitting these in older versions of Matlab be available soon? Have we missed an obvious step which is making our model not converge at 85% of the positions? Thank you for your help, Best Wishes, Cathy X = [ones(length(M),1) M(:,1) Mat(:,1) Mat(:,1).*M(:,1) Mat(:,2) Mat(:,2).*M(:,1) Mat(:,3) Mat(:,3).*M(:,1) M(:,3)-1 M(:,4)]; Quoting Jorge jbernal0...@yahoo.es on Fri, 21 Jun 2013 10:42:11 -0700: Hi Cathy You should put a comma between X and [1 2] lhstats = lme_mass_fit_vw(X, [1 2],ni,lhcortex); The model with a single random effect for the intercept term must always converge: lhstats = lme_mass_fit_vw(X, [1],ni,lhcortex); Can you tell me with words what the columns of your design matrix are? How many subjects and how many repeated measures for each subject do you have? Best -Jorge Sent from my iPad On Jun 21, 2013, at 4:53, Catherine Bois c.b...@sms.ed.ac.uk wrote: Dear Jorge/freesurfer group, I am using the scripts you sent me that do not require the newer version of matlab, and now using a computer that has the Statistics toolbox. I can get the scripts (with the suffix 1) to run with; lhstats = lme_mass_fit_vw(X[1 2],ni,lhcortex);) however it fails to reach convergence at most vertices. We have tried simplifying the model to include only one random effect at a time, however the problem persists. Our design matrix is as follows; X = [ones(length(M),1) M(:,1) Mat(:,1) Mat(:,1).*M(:,1) Mat(:,2) Mat(:,2).*M(:,1) Mat(:,3) Mat(:,3).*M(:,1) M(:,3)-1 M(:,4)]; I have read on the mailing list that non-convergence at some vertices is normal, however what we are getting far exceeds 10%. Any help on this matter would be greatly appreciated! Best Wishes, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ Freesurfer mailing list 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] mri_glimfit paired analysis
Dear FreeSurfers I'm using Freesurfer 5.1 on Ubuntu 12.04 LTS. Currently running paired analysis as described here https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis After mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \ --C mean.mtx \ --C age.mtx I've got an error ERROR: you must use '--surface subject hemi' with surface data. Any idea how to fix it? Below is the full output: utente@RM-user:~/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis$ mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --C age.mtx gdfReadHeader: reading paired-diff.fsgd INFO: ignoring tag ,9 INFO: ignoring tag ,9 INFO: ignoring tag ,3 INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 57 11.0454 Class Means of each Continuous Variable 1 Main 57. INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis cmdline mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --C age.mtx sysname Linux hostname RM-user machine x86_64 user utente FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis/lh.paired-diff.thickness.sm05.mgh logyflag 0 usedti 0 FSGD paired-diff.fsgd glmdir lh.paired-diff IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.paired-diff Loading y from /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis/lh.paired-diff.thickness.sm05.mgh ERROR: you must use '--surface subject hemi' with surface data Thanks for yuo help Gayane ___ Freesurfer mailing list 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.
Re: [Freesurfer] Help with QDEC error
Hi Nick and Doug, Can you suggest an alternative way if QDEC is unable to handle a single group? I would like to run these analyses to address reviewers comments. Best, Manish From: Douglas Greve gr...@nmr.mgh.harvard.edu To: Manish Dalwani manishdalw...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 20, 2013 11:16 PM Subject: Re: [Freesurfer] Help with QDEC error I thought it would have worked with a single group. Maybe Nick knows of the top of his head. doug On 6/20/13 12:36 PM, Manish Dalwani wrote: Hi Doug and Freesurfers, I realized that I hadn't updated my group levels to one group. However, when I do that..the qdec complains about group.level having at minimum two levels. How can I run (using QDEC) single group regression? Thanks, Manish From: Manish Dalwani manishdalw...@yahoo.com To: Douglas Greve gr...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 20, 2013 1:26 PM Subject: Re: [Freesurfer] Help with QDEC error Hi Doug, I was out of town for a conference. Please see my attachments. I have the log file and screenshots of ill-matrix conditioning. Thanks for your help! Manish From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Saturday, June 15, 2013 11:09 AM Subject: Re: [Freesurfer] Help with QDEC error Can you send the mri_glmfit.log file from /Applications/freesurfer/subjects/qdec/Untitled ? doug On 6/14/13 4:57 PM, Manish Dalwani wrote: Hello Freesurfers, I am trying to run regression analyses within patients and one variable of interest which adjusting for the nuisance variables age, IQ, thickness. When i select the group and the CD (variable of interest) and run analyses (DODS), I get the following error: Qdec 1.4 (Qdec1.4) Type: Error Time: Fri Jun 14 14:49:37 2013 Description: Error in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat Please advice! Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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@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@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] Is there any way of finding out RESEL number in the GLM output?
Hello Freesurfer users, I'd hope to know the RESEL number in my group GLM analysis data. I can calculate the number of vertices and also see the fwhm.dat in the ouput GLM folder, but I wonder if there is anyway of finding out RESEL size if freesurfer also provides that info like SPM does. -Glen ___ Freesurfer mailing list 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] retinotopy betas
Hi, I am examining the affect a metal artifact has on fMRI data, and I am using Eccentricity mapping with the retinotopy analysis in FSFast. I was recently asked to switch from examining the difference in the fsig to examining the difference in the betas. I opened up beta.nii.gz and I can see that it has a size of: 1 #of vertices 1 39 Can you explain to me, how I figure out where each of the 39 come from (and possibly point me to which of these might be appropriate to use?)? Thank You, Dan ___ Freesurfer mailing list 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] [FreeSurfer] Freeview: Invalid drawable
Dear Koen, Freeview returns 8 lines of the error message invalid drawable whenever executed. The messages are as follows 2013-06-24 14:24:57.930 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.931 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.944 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.945 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.957 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.958 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.971 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.972 Freeview[1937:303] invalid drawable In the $FREESURFER_HOME directory, I tried sed -i 's/CA2_3/CA2\/3/g' FreeSurferColorLUT.txt sed -i 's/CA4_DG/CA4\/DG/g' FreeSurferColorLUT.txt as you suggested in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22276.html(content copied at the end of this email) I checked in FreeSurferColorLUT.txt and made sure all CA2_3 was changed into CA2\3, all CA4_DG into CA4\DG, but the problem still persists. My computer is Mac OS X version 10.8.2. I downloaded freesurfer-Darwin-lion-stable-pub-v5.3.0.dmgftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg Would you please give me some guidance on how to fix the problem? Thank you very much! Sincerely, Ye Tian Hi Ed, It seems that the 5.1.0 release for the Mac was composed two days after the one for Linux, and during exactly those two days one of us made a change to the file $FREESURFER_HOME/FreeSurferColorLUT.txt. To correct this issue, please make a back-up copy of your FreeSurferColorLUT.txt file, and execute the following commands: cd $FREESURFER_HOME sed -i s/CA2_3/CA2\/3/g FreeSurferColorLUT.txt sed -i s/CA4_DG/CA4\/DG/g FreeSurferColorLUT.txt Thanks, Koen On Wed, Apr 4, 2012 at 9:32 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: I have downloaded the file freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg, date 26/05/2011. Ed On 4 Apr 2012, at 13:09, Koen Van Leemput wrote: OK, I see why this is not working. We've been changing some name conventions in our internal FreeSurfer repository after the public release of version 5.1, and somehow you managed to get an incompletely updated version. It appears from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0 that some versions for the Mac were updated *after* the release date (24 May 2011), so I'll check with the engineers what exactly happened. Do you remember which file you downloaded? Thanks, Koen On Wed, Apr 4, 2012 at 6:59 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi Koen, No worries. The result of grep is: 500 right_CA2_3 17 85 136 0 550 left_CA2_3 17 85 137 0 Ed On 4 Apr 2012, at 12:41, Koen Van Leemput wrote: Hi Ed, Can you please do grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt and let me know what the result is? Thanks, and sorry this seems so difficult to sort out. Koen On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi Koen, As already mentioned, I'm using v5.1.0, Mac Intel Leopard version. The voxel values of posterior_left_CA2-3.mgz and posterior_right_CA2-3.mgz are between 0 and 255, if that is what you mean by results. By the way: I always get the 8 lines with invalid drawable messages from freeview. Ed On 3 Apr 2012, at 21:29, Koen Van Leemput wrote: Hi Ed, What version of the FreeSurfer build are you using? Also, could you please let me know what the result is of ls posterior_left_CA2*? Thanks, Koen On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi, I followed the instructions to visualize the hippocampal subfield segmentation by entering the command (in the subject's mri directory) freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt and got the following messages: 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index
[Freesurfer] infant .tiff templates
Hello freesurfers, I am currently attempting to create my own .tiff templates for a series of infant fMRI's (neonates, 1 yr olds, and 2 yr olds). I currently have the templates in .nii.gz, .mgz, and .img/.hdr formats. Is there any easy way to convert from one of these formats to a .tiff image to use as an actual template for reconstruction with FreeSurfer? If so, would the conversion distort/ruin the template? Thank you! - Mark Plantz ___ Freesurfer mailing list 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] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh
Hi all, I am getting error messages while running kvlQuantifyHippocampalSubfieldSegmentations.sh, similar to the error mentioned in an earlier email (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24430.html). We did use the -hippo-subfields flag for all of our subjects first, and the output was 20 left and right subfield mgz files (it completed without any errors). The subjects had already undergone the standard volumetric FreeSurfer pipeline and therefore we ran the command: recon-all -s subjectID -hippo-subfields. The error message for kvlQuantifyHippocampalSubfieldSegmentation that I'm getting is: resultsDirectory ***/HIPPOCAMPAL_TEST cd ***/HIPPOCAMPAL_TEST resultsDirectory ***/HIPPOCAMPAL_TEST startIndex: 1 endIndex: 2 cd subjectID_recon/ Quantifying subject ID_recon left Doing left side cd left cd segmentationWithoutPartialVolumingLog kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x46b690): Can't find/open file: posterior_Left-Hippocampus.mgz kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 50779 Abort trap kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt Is there anything else that we are missing and should run? Thanks! ___ Freesurfer mailing list 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.
Re: [Freesurfer] infant .tiff templates
Hi Mark can you clarify what you mean? What template are you referring to? Bruec On Mon, 24 Jun 2013, Mark Plantz wrote: Hello freesurfers, I am currently attempting to create my own .tiff templates for a series of infant fMRI's (neonates, 1 yr olds, and 2 yr olds). I currently have the templates in .nii.gz, .mgz, and .img/.hdr formats. Is there any easy way to convert from one of these formats to a .tiff image to use as an actual template for reconstruction with FreeSurfer? If so, would the conversion distort/ruin the template? Thank you! - Mark Plantz ___ Freesurfer mailing list 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.
Re: [Freesurfer] Multiple inputs into recon-all -i
Hi Ye you only need to give it a single file from each run and it will find the rest. The only time you use -i more than once is if you acquired more than 1 T1-weighted volume. Definitely don't give it all the files that make up the same volume cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear David, I wonder whether there is a short cut for recon-all -s Barbara -i /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i /path_to_data/scan100.dicom Recon-all -i takes only a single file as an input. A typical user, however, has hundreds of files for a particular subject. For example, the directory Barbara may have 100 scans. Therefore, the above command is necessary to include all the scans. I understand that I can write loops to a text file and then copy and paste to command line. However, I wonder whether there is a simpler way to input several files or even a directory to recon-all. Thank you very much! Sincerely, Ye ___ Freesurfer mailing list 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.
Re: [Freesurfer] Multiple inputs into recon-all -i
Dear Bruce, Thank you very much for your suggestion, but I am afraid that I still don't quite understand you. In order to make it simple, suppose I have two files, Barba001.IMA and Barba002.IMA, coming directly from the scanner. Now if I enter *recon-all -s Barba -i Barba001.IMA* from the command line, I am only able to find *001.mgz* in the Barba/mri/orig. Aren't I supposed to to find 001.mgz and 002.mgz? Thank you so much! Sincerely, Ye On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ye you only need to give it a single file from each run and it will find the rest. The only time you use -i more than once is if you acquired more than 1 T1-weighted volume. Definitely don't give it all the files that make up the same volume cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear David, I wonder whether there is a short cut for recon-all -s Barbara -i /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i /path_to_data/scan100.dicom Recon-all -i takes only a single file as an input. A typical user, however, has hundreds of files for a particular subject. For example, the directory Barbara may have 100 scans. Therefore, the above command is necessary to include all the scans. I understand that I can write loops to a text file and then copy and paste to command line. However, I wonder whether there is a simpler way to input several files or even a directory to recon-all. Thank you very much! Sincerely, Ye 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/**compliancelinehttp://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@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.
Re: [Freesurfer] Multiple inputs into recon-all -i
Hi Ye, you would never have two files, as each file represents one image, or slice from a sequence. So you might have two sequences of files, say Barba001-1.img, Barba001-2.img... Barba001-256.ima, and Baraba002-1.ima, Barba002-2.ima Barba002-256.ima. Then you would use -i twice, once with *one* file from each series (it wouldn't matter which one). cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear Bruce, Thank you very much for your suggestion, but I am afraid that I still don't quite understand you. In order to make it simple, suppose I have two files, Barba001.IMA and Barba002.IMA, coming directly from the scanner. Now if I enter recon-all -s Barba -i Barba001.IMA from the command line, I am only able to find 001.mgz in the Barba/mri/orig. Aren't I supposed to to find 001.mgz and 002.mgz? Thank you so much! Sincerely, Ye On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ye you only need to give it a single file from each run and it will find the rest. The only time you use -i more than once is if you acquired more than 1 T1-weighted volume. Definitely don't give it all the files that make up the same volume cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear David, I wonder whether there is a short cut for recon-all -s Barbara -i /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i /path_to_data/scan100.dicom Recon-all -i takes only a single file as an input. A typical user, however, has hundreds of files for a particular subject. For example, the directory Barbara may have 100 scans. Therefore, the above command is necessary to include all the scans. I understand that I can write loops to a text file and then copy and paste to command line. However, I wonder whether there is a simpler way to input several files or even a directory to recon-all. Thank you very much! Sincerely, Ye 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@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.
Re: [Freesurfer] Multiple inputs into recon-all -i
Dear Bruce, Thank you very much! Sincerely, Ye On Mon, Jun 24, 2013 at 7:32 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ye, you would never have two files, as each file represents one image, or slice from a sequence. So you might have two sequences of files, say Barba001-1.img, Barba001-2.img... Barba001-256.ima, and Baraba002-1.ima, Barba002-2.ima Barba002-256.ima. Then you would use -i twice, once with *one* file from each series (it wouldn't matter which one). cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear Bruce, Thank you very much for your suggestion, but I am afraid that I still don't quite understand you. In order to make it simple, suppose I have two files, Barba001.IMA and Barba002.IMA, coming directly from the scanner. Now if I enter recon-all -s Barba -i Barba001.IMA from the command line, I am only able to find 001.mgz in the Barba/mri/orig. Aren't I supposed to to find 001.mgz and 002.mgz? Thank you so much! Sincerely, Ye On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ye you only need to give it a single file from each run and it will find the rest. The only time you use -i more than once is if you acquired more than 1 T1-weighted volume. Definitely don't give it all the files that make up the same volume cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear David, I wonder whether there is a short cut for recon-all -s Barbara -i /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i /path_to_data/scan100.dicom Recon-all -i takes only a single file as an input. A typical user, however, has hundreds of files for a particular subject. For example, the directory Barbara may have 100 scans. Therefore, the above command is necessary to include all the scans. I understand that I can write loops to a text file and then copy and paste to command line. However, I wonder whether there is a simpler way to input several files or even a directory to recon-all. Thank you very much! Sincerely, Ye 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/**compliancelinehttp://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@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.
Re: [Freesurfer] Fwd: DTI questions
Sorry, can't open the image. On Sun, 23 Jun 2013, Rotem Saar wrote: Hi there, Long time:). Well I wrote to the list several times regarding high FA values I got when performing DTI analysis. Today we know that the problem was an additional direction (we had 17 directions instead of 16 - we used a Philips scanner,1.5T). So we deleted the additional slices and the high values indeed disappeared, but then another problem came up (tried several subjects so the problem is not specific to a subject) - I noticed an artifact that I can't explain - please see the attached pictures. This artifact existed even before I deleted the additional slices, also - I see the artifact also when loading the masked volume...It is cyclic - run over all slices... any ideas ? I'm using version 5.2 and I know the command lines are correct (send it to u in the past). Thanks for your help Rotem ___ Freesurfer mailing list 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.
Re: [Freesurfer] Fwd: DTI questions
Hi Rotem - No problem. Were these scans by any chance acquired with a coronal slice prescription? In the axial views that you sent, the artifact that you're pointing to looks like misalignment between consecutive coronal slices, which could be due to head motion. a.y On Tue, 25 Jun 2013, Rotem Saar wrote: Dear Anastasia, I tried several times to upload these images in a non-compressed way, but they were too big and my posts were rejected, with no opportunity for any other upload way. Is there any other way for me to upload it so that everyone can see it ? Attached are the images in a non-compressed fashion. I will be very happy if u will have a look, and post your answer to me and the list to save some time, until I will be able to consider another way to upload them. I know that we should write to all the list, but at the moment if the images are not visible this won't help - so I will really appreciate if u will have a look but also tell me what is the best way to upload them so that all list members will be able to see them. Thank u very much for your help. Rotem 2013/6/25 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Sorry, can't open the image. On Sun, 23 Jun 2013, Rotem Saar wrote: Hi there, Long time:). Well I wrote to the list several times regarding high FA values I got when performing DTI analysis. Today we know that the problem was an additional direction (we had 17 directions instead of 16 - we used a Philips scanner,1.5T). So we deleted the additional slices and the high values indeed disappeared, but then another problem came up (tried several subjects so the problem is not specific to a subject) - I noticed an artifact that I can't explain - please see the attached pictures. This artifact existed even before I deleted the additional slices, also - I see the artifact also when loading the masked volume...It is cyclic - run over all slices... any ideas ? I'm using version 5.2 and I know the command lines are correct (send it to u in the past). Thanks for your help Rotem 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@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.
