Re: [Freesurfer] Antw: Re: [tracula] error running trac-all -prep
Hi Anastasia, Here are the bvec and bval files you asked me about. Sincerely, Florian Anastasia Yendiki 18.08.13 22.52 Uhr Hi Florian - Can you please also attach the bvecs/bvals files from the dmri directory? Thanks, a.y On Sun, 18 Aug 2013, Borsodi Florian wrote: Hi Anastasia, Thanks for your help. I renamed the directories and reran trac-all. It worked for the moment. However, then I got another error: bvecs and bvals don't have the same number of entries. I don't know why, because they actually have the same number of entries. I attached the logfile so that you may see what is going on. The error occours at line 1463. Thank you in advance for your help. Sincerely, Florian Anastasia Yendiki 15.08.13 18.01 Uhr Hi Florian - I see what's going on. Can you please rename the directory /data/physics/florian/nii into something that doesn't include nii, and rerun? Because nii is a file extension, this confuses some of the scripts. Thanks, a.y On Thu, 15 Aug 2013, Borsodi Florian wrote: Hi Anastasia I ran the command you sent me and it runs without any errors. I also attached the command line for you. Furthermore i ran data with 12 diffusion directions and i keep getting the same kind of problems. sincerely Florian Anastasia Yendiki 02.08.13 19.59 Uhr Hi Florian - Can you please run this command directly on the command line and see if there are any errors? flip4fsl /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz Thanks, a.y On Fri, 2 Aug 2013, Borsodi Florian wrote: Hi Anastasia Thank you for your answer. Yes, those files exist. I also extracted the bvec an bval files with anotther software then dcm2nii and i keep getting the same kind of error. Also, about the 6 diffusion direction, those data i sent you, are just testdata for running tracula. sincerely Florian Anastasia Yendiki 02.08.13 0.41 Uhr Hi Florian - Do these files exist? /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvec s /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bval s The format of the bvecs and bvals that you sent seems fine, but (and this has nothing to do with the error you're getting) I have to warn you that you may not be able to get good results running probabilistic tractography on this data. It looks like you're acquiring the same 6 diffusion directions, repeated 8 times. Six directions is the absolute minimum for reconstructing the tensor model, but will probably not be sufficient for the crossing fiber model that bedpostx reconstructs (and is used by tracula). Your scan time is better spent acquiring 48 different directions, rather than the same 6 directions 8 times. a.y On Mon, 29 Jul 2013, Borsodi Florian wrote: Hello, I have been trying to run tracula on my data and i keep getting the same kind of error repeatedly. For my imput I am using dicoms from a Siemens scanner with a stadard diffusion protocol. However, tracula cannot read the bvec and bval data out of the dicom header. Therefore, I implemented bvec and bval files into the config file. After doing so, I got the error which says that tracula cannot find the dwi_orig_flip.mghdti.bvecs and dwi_orig_flip.mghdti.bvals files. I have tried many options, but still cannot find a solution. I am hoping to get some troubleshooting help. I have atteched my log- and config- files, as well as my bvec and bval files. To uphold patient confidentiality, I have encode the name patient's data as AA. I believe the problems are the bvec and bval files or their structures. The log-file lete me assume this, especially the lines 202 - 205, 264 - 268 and 1480 - 1484. Thank you in advance for your help, and your speedy response. With kind regards, Florian Borsodi Department of Neurology Medical University of Graz 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 bvecs Description: Binary data bvals Description: Binary data ___ Freesurfer mailing list
[Freesurfer] error for autorecon3
Hi all, I am trying to run recon-all on a structural for one of my subjects, but freesurfer exited with errors during the last few stages (the ones covered by autorecon-3). It appears that it is just missing some label - the problem occurs at the following stage: painting output onto subject ME. processing subject lh.EC_average... MRISread (filename) could not open file I've used freesurfer before, same subject directory, but didn't get this error - it appears from the path after the MRISread command that it is just the subject directory, but not the directory for this particular subject. It appears freesurfer is looking for this file, which it can't find: /home/virtualuser/freesurfer/s_sub/lh.EC_average/surf/lh.sphere.reg where /home/virtualuser/freesurfer/s_sub is my subject directory. Can anyone advise as to how to fix this? Any help would be much appreciated. Best Luzia ___ 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] Orientation/Primary-Slice-Direction
Hello freesurfers, I have an image that is in RAS orientation with the axial primary slice direction. Is there anyway to change this to LIA orientation with the coronal primary slice direction? I am assuming mri_convert would work, but I'm not sure which flags to use. Thanks in advance. MP ___ 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] Qdec: regression with different numbers of variables
Dear Doug, Would you please shine some light on what quantities are being plotted in those statistical maps of QDEC? Some linear combination of the columns of the design matrix? Also, what is the default design matrix? Thank you very much! Sincerely, Ye On Tue, Aug 13, 2013 at 11:45 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: 1 and 3 are the same model. Calling a variable a nuisance factor is just a description. The model is actually y = age*meditation*b1 + meditation*b2 + err = y_hat + err doug On 8/13/13 6:12 PM, ye tian wrote: Dear Freesurfers, I am studying cortical thickness as a function of age (continuous) and meditation practice (categorical, level1=Normal, level2=TM). I have three separate cases of qdec, regression1, regression2 and regression3. Regression1: Discrete (Fixed Factor) = meditation; Continuous (Covariate) = age Regression2: Discrete (Fixed Factor) = meditation; Regression3: Discrete (Fixed Factor) = meditation; Nuisance Factor = age For the question Does the average thickness differ between Normal and TM?, Regression1 and Regression3 have identical result, which is different from Regression2, i.e., (1 = 3 !=2 ). May I infer from this result the following about qdec: 1) Regression1 and Regression3 both fit cortical thickness,y, to the model y = b0 + age*b1 + meditation*b2 + err = y_hat + err Regression2 fits: y = b0 + b2*meditation + err = y_hat + err 2) Some function of y_hat goes into the average thickness, hence the difference between 2 and the others. However, what role does Nuisance Factor play in this case? Thank you very much! Sincerely, Ye ___ 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. ___ 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] error for autorecon3
Hi Luzia the lh.EC_average should be a symlink to $FREESURFER_HOME/subjects/lh.EC_average if it doesn't exist, create it with ln -s cheers Bruce On Mon, 19 Aug 2013, Troebinger, Luzia wrote: Hi all, I am trying to run recon-all on a structural for one of my subjects, but freesurfer exited with errors during the last few stages (the ones covered by autorecon-3). It appears that it is just missing some label - the problem occurs at the following stage: painting output onto subject ME. processing subject lh.EC_average... MRISread (filename) could not open file I've used freesurfer before, same subject directory, but didn't get this error - it appears from the path after the MRISread command that it is just the subject directory, but not the directory for this particular subject. It appears freesurfer is looking for this file, which it can't find: /home/virtualuser/freesurfer/s_sub/lh.EC_average/surf/lh.sphere.reg where /home/virtualuser/freesurfer/s_sub is my subject directory. Can anyone advise as to how to fix this? Any help would be much appreciated. Best Luzia ___ 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] Trouble with mris_label2annot
Your original labels are not on fsaverage. You need to transfer them to fsaverage using mri_label2label. That should fix your first problem. The 2nd should be fixed by having your ctab go from 0 to 58 with 0 being the unknown label doug On 08/18/2013 02:51 PM, Stephen Politzer-Ahles wrote: Hello, I have a set of custom labels and I want to plot them all at once on one brain, so I'm trying to use mris_label2annot for that. However, I'm getting several problems. Here is an example of what I get: http://i.imgur.com/Sw1Z9UT.png The labels I'm using were originally defined on a decimated source space (that was created using the MNE toolbox), so it's normal that most of them show up as lots of dots rather than contiguous areas. However, I don't know why some of them actually are showing up as contiguous areas; when I plot the labels one by one, all of them show up as series of dots rather than contiguous areas, so it seems that creating the annotation is messing something up. I also have a few other problems that you can't see in the image. Firstly (and most seriously), the locations of the labels that show up when I plot this annotation do not at all match where the labels actually are--that is, if I hover my mouse over one of the labels in this, it doesn't match where the label actually should be if I plot that label by itself. Secondly, there seems to be some indexing issue with my color lookup table--I have 58 labels per hemisphere, so I created a color table that starts at label 0 and goes up to 57 (as per the example at http://ftp.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles and the automatically-generated annotations such as lh.aparc2009s.annot). In my color lookup table, label 0 is called 'amygdala' and label 1 is called 'anteriorcommisure'. But when I actually run mris_label2annot, the output seems to suggest that the program is 1-indexed instead of 0-indexed (because it skips the 0th label, andlooks for the 57th label, see output snippet below): Reading ctab /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab Number of ctab entries 58 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ ... cmdline mris_label2annot --ctab /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab --subject fsaverage --annot MRATparc --hemi lh --l lh.amygdala.label --l lh.anteriorcommissure.label --l lh.anteriornucleus.label --l lh.ba1.label --l lh.ba10.label --l lh.ba11.label --l lh.ba13.label --l lh.ba17.label --l lh.ba18.label --l lh.ba19.label --l lh.ba2.label --l lh.ba20.label --l lh.ba21.label --l lh.ba22.label --l lh.ba23.label --l lh.ba24.label --l lh.ba25.label --l lh.ba27.label --l lh.ba28.label --l lh.ba29.label --l lh.ba3.label --l lh.ba30.label --l lh.ba31.label --l lh.ba32.label --l lh.ba33.label --l lh.ba34.label --l lh.ba35.label --l lh.ba36.label --l lh.ba37.label --l lh.ba38.label --l lh.ba39.label --l lh.ba4.label --l lh.ba40.label --l lh.ba41.label --l lh.ba42.label --l lh.ba43.label --l lh.ba44.label --l lh.ba45.label --l lh.ba46.label --l lh.ba47.label --l lh.ba5.label --l lh.ba6.label --l lh.ba7.label --l lh.ba8.label --l lh.ba9.label --l lh.caudatebody.label --l lh.caudatehead.label --l lh.caudatetail.label --l lh.corpuscallosum.label --l lh.culmen.label --l lh.declive.label --l lh.hippocampus.label --l lh.hypothalamus.label --l lh.mammillarybody.label --l lh.medialdorsalnucleus.label --l lh.optictract.label --l lh.pulvinar.label --l lh.putamen.label ... subject fsaverage hemilh SUBJECTS_DIR /media/LAPTOP_HD/WW3_newanalysis/subjects ColorTable /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab AnnotName MRATparc nlables 58 LabelThresh 0 0.00 Loading /media/LAPTOP_HD/WW3_newanalysis/subjects/fsaverage/surf/lh.orig 1 3988503 anteriorcommissure 2 11811863 anteriornucleus 3 3957823 ba10 ... 56 1326221 pulvinar 57 14423183 putamen 58 -1 NOT_FOUND Does anyone have suggestions about any or all of these issues? Thank you, Steve Politzer-Ahles Stephen Politzer-Ahles New York University, Abu Dhabi Psychology Department http://www.nyu.edu/projects/politzer-ahles/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ 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
[Freesurfer] R: Re: Statistical concerns
Dear Doug, thank you very much for your reply!Point c, is now ok. Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 4-ago-2013 20.34 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Statistical concerns On 8/1/13 7:56 AM, std...@virgilio.it wrote: Hi list, I have some questions please. 1- I have carried out Monte Carlo Simulation to assess the difference among three groups (23, 24 and 32 subjects). Main results were confirmed also by FDR, but I prefer to shown the Monte Carlo becouse it better describes my thesis. Recently I have submitted my paper but a referee asked me Why use cluster based Monte Carlo methods for correction of multiple comparisons instead of the more conventional vertex-wise FDR correction? I suspect the former is much less conservative than the latter. It would be interesting to know the results for FDR corrected thresholds (p0.05), and whether the present results would remain statistically 'active'. Now, I'm looking literature and I'm noting that several recent articles published on top journals used Monte Carlo Simulation (Ehrlich et al., 2013 Schizophr Bull.; Sasamoto et al., 2013 Schizophr Bull). What do you think about it? How do you advise to reply to the referee? I'd like to show Monte Carlo results. This is a very surprising request by the reviewer. FDR is hardly conventional, and the brain imaging community has been using clusterwise correction for 20 years. I'm not even sure what voxelwise FDR is. Is that different than the one introduced by Genovese in 2002? As for how to respond to the reviewer, I'm not sure. You can certainly make a case that doing the clusterwise correction is the industry standard. You can also site a paper out of the Friston group from a few years back critisizing the Genovese-style FDR. Have you applied the Genovese-style FDR that we offer in FS? If that works out, then there is no need to fight with the reviewer. 2- I should do also correlation analysis. I'm using QDEC as recommanded in guideliness (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview). In one group, after fsgd creation, I'm performing correlation analysis between thickness and neuropsychiatric test scores (it has been put in covariete windows-it should be dipendent factor). I'm also putting some nuisance factors (they should be dipendent factor in the regression analysis) to exclude the their effect on data. a- Is this procedure corrected? b- Is corrected to talk regression analysis in the text of my manuscript? c- Is corrected whether I explain this correlation analysis as reported in the description performed above? I'm confused. If you are using qdec, then you put your factors (which are independent) in the qdec table, not in the FSGD file. Otherwise the procedure looks correct and you can talk about regression analysis in your ms. I don't understand (c). doug Thank you very much, Stefano ___ 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.
Re: [Freesurfer] Orientation/Primary-Slice-Direction
try setting the orientation string to LIA On 08/19/2013 11:15 AM, Mark Plantz wrote: Hello freesurfers, I have an image that is in RAS orientation with the axial primary slice direction. Is there anyway to change this to LIA orientation with the coronal primary slice direction? I am assuming mri_convert would work, but I'm not sure which flags to use. Thanks in advance. MP ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ 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] [Tracula] error running trac-all –path –c Configuration_file.txt
Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory? ___ 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] Qdec: regression with different numbers of variables
Dear Doug, If I only have two groups, does the statistical test reduce to a two-tail t-test? Sorry, I meant to ask what the default contrast is, meaning what the contrast is when I specify no nuisance factor? Is there an official document where the QDEC setup is gone over systematically? Thank you very much! Sincerely, Ye On Mon, Aug 19, 2013 at 11:04 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: -log10(p) which p is the pvalue for the statistical test. The color is signed by the test. On 08/19/2013 11:19 AM, ye tian wrote: Dear Doug, Would you please shine some light on what quantities are being plotted in those statistical maps of QDEC? Some linear combination of the columns of the design matrix? Also, what is the default design matrix? Thank you very much! Sincerely, Ye On Tue, Aug 13, 2013 at 11:45 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: 1 and 3 are the same model. Calling a variable a nuisance factor is just a description. The model is actually y = age*meditation*b1 + meditation*b2 + err = y_hat + err doug On 8/13/13 6:12 PM, ye tian wrote: Dear Freesurfers, I am studying cortical thickness as a function of age (continuous) and meditation practice (categorical, level1=Normal, level2=TM). I have three separate cases of qdec, regression1, regression2 and regression3. Regression1: Discrete (Fixed Factor) = meditation; Continuous (Covariate) = age Regression2: Discrete (Fixed Factor) = meditation; Regression3: Discrete (Fixed Factor) = meditation; Nuisance Factor = age For the question Does the average thickness differ between Normal and TM?, Regression1 and Regression3 have identical result, which is different from Regression2, i.e., (1 = 3 !=2 ). May I infer from this result the following about qdec: 1) Regression1 and Regression3 both fit cortical thickness,y, to the model y = b0 + age*b1 + meditation*b2 + err = y_hat + err Regression2 fits: y = b0 + b2*meditation + err = y_hat + err 2) Some function of y_hat goes into the average thickness, hence the difference between 2 and the others. However, what role does Nuisance Factor play in this case? Thank you very much! Sincerely, Ye __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Qdec: regression with different numbers of variables
QDEC creates a sentence that describes each contrast. Is that sentence not clear? I think the only other docs we have for QDEC are the tutorial. doug On 08/19/2013 12:19 PM, ye tian wrote: Dear Doug, If I only have two groups, does the statistical test reduce to a two-tail t-test? Sorry, I meant to ask what the default contrast is, meaning what the contrast is when I specify no nuisance factor? Is there an official document where the QDEC setup is gone over systematically? Thank you very much! Sincerely, Ye On Mon, Aug 19, 2013 at 11:04 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: -log10(p) which p is the pvalue for the statistical test. The color is signed by the test. On 08/19/2013 11:19 AM, ye tian wrote: Dear Doug, Would you please shine some light on what quantities are being plotted in those statistical maps of QDEC? Some linear combination of the columns of the design matrix? Also, what is the default design matrix? Thank you very much! Sincerely, Ye On Tue, Aug 13, 2013 at 11:45 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: 1 and 3 are the same model. Calling a variable a nuisance factor is just a description. The model is actually y = age*meditation*b1 + meditation*b2 + err = y_hat + err doug On 8/13/13 6:12 PM, ye tian wrote: Dear Freesurfers, I am studying cortical thickness as a function of age (continuous) and meditation practice (categorical, level1=Normal, level2=TM). I have three separate cases of qdec, regression1, regression2 and regression3. Regression1: Discrete (Fixed Factor) = meditation; Continuous (Covariate) = age Regression2: Discrete (Fixed Factor) = meditation; Regression3: Discrete (Fixed Factor) = meditation; Nuisance Factor = age For the question Does the average thickness differ between Normal and TM?, Regression1 and Regression3 have identical result, which is different from Regression2, i.e., (1 = 3 !=2 ). May I infer from this result the following about qdec: 1) Regression1 and Regression3 both fit cortical thickness,y, to the model y = b0 + age*b1 + meditation*b2 + err = y_hat + err Regression2 fits: y = b0 + b2*meditation + err = y_hat + err 2) Some function of y_hat goes into the average thickness, hence the difference between 2 and the others. However, what role does Nuisance Factor play in this case? Thank you very much! Sincerely, Ye ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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
[Freesurfer] Two Inquiries
1. Segmentation of partial brain Dear FreeSurfers, 1. Can I expect recon-all to work on a T1W image where only part of the brain is in FOV? The obvious answer is that I should just try, but it would help to know in case I get unexpected results. Perhaps a more appropriate question is: what should I expect to work and what should I expect to fail. Thank you, -- 2. Rotated segmentation Dear FreeSurfers, I start with a T1W image in NIFTI format. After running recon-all, I use mri_convert to convert aseg.mgz to aseg.nii. This aseg.nii image does not overlay the original T1W. It is slightly rotated. Is it normal? If I would like to make it overlay what should I do? Register using flirt? Thank you, -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine ___ 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] Two Inquiries
On 08/19/2013 12:42 PM, Liane Hunter wrote: 1. Segmentation of partial brain Dear FreeSurfers, 1. Can I expect recon-all to work on a T1W image where only part of the brain is in FOV? The obvious answer is that I should just try, but it would help to know in case I get unexpected results. Perhaps a more appropriate question is: what should I expect to work and what should I expect to fail. I doubt it will work. I the regsitrations will likely fail. Thank you, -- 2. Rotated segmentation Dear FreeSurfers, I start with a T1W image in NIFTI format. After running recon-all, I use mri_convert to convert aseg.mgz to aseg.nii. This aseg.nii image does not overlay the original T1W. It is slightly rotated. Is it normal? If I would like to make it overlay what should I do? Register using flirt? See this page http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat Thank you, -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ 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] [Tracula] error running trac-all –path –c Configuration_file.txt
From: Francesco Siciliano Sent: Monday, August 19, 2013 12:54 PM To: Francesco Siciliano Subject: RE: [Tracula] error running trac-all –path –c Configuration_file.txt I also noticed that even on those that appeared to finish, there was no dpath folder. Any help would be greatly appreciated! Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155 From: Francesco Siciliano Sent: Monday, August 19, 2013 12:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Tracula] error running trac-all –path –c Configuration_file.txt Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory? ___ 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] few questions regarding qdec
On 08/16/2013 05:02 PM, Binod Thapa-Chhetry wrote: HI all, We had submitted a paper based on cortical thickness analysis in Qdec. The reviewer's had couple concerns regarding the QDec analysis. We would appreciate your help to address/resolve those issues. Here are the concerns: (1) What was the rationale of using 10mm smoothing? The typical fMRI values for volumteric work is 2-3 x the original voxel size. What's the reason for this value? Our response so far: A smoothing kernel of 10 mm was chosen because this setting had been published recently in articles that performed similar analyses. 10 mm therefore was a typical parameter for this type of analysis. This setting was also the default in the QDEC GUI, also suggesting that it was a typical setting. We only performed analyses of the data for this project using this setting and did not iteratively test multiple kernel widths. Also, the FWHM for cortical thickness analyses is somewhat larger than that used in fMRI analyses because it is applied to surface, as opposed to volume-based data. Surface based data are not prone to the same artifacts of including white matter, csf or brain tissue on the other side of a sulcus as volume-based data are. I think this is a good answer for a question that is not entirely fair. Aside from a few arguments about making GRF work, no one has ever had much of a justification for the particular choice of FWHM. It is just traditional at this point. You might point out that more smoothing is generally considered worse and that 10mm on the surface is much less than 10mm in the volume and people use 10mm in the volume is not unusual. (2) What's the p-value to get in for a cluster-wise analysis and what size is a significant cluster? It's important to know these non cluster-wise values to get a sense of the parameters that determine significance. Our response so far: QDEC does not have a parameter that can be adjusted for cluster size or extent as other whole brain analyses such as Statistical Parametric Mapping do. The researcher can only indicate a statistical cutoff. We used a p value cutoff of 0.05 after a correction for multiple comparisons that was based on the Monte Carlo permutation cluster analysis with 10,000 iterations. Additionally, our findings comprise of pretty large clusters. This obviates the reason for cluster-thresholding based on size. I'm not sure what the reviewer is asking. Is he/she asking for the cluster-forming, ie, voxel-wise, threshold? Or the p-value threshold for the cluster that you used to report clusters? You should report both. Both can be set in the QDEC GUI. I think the defaults are .01 and .05 respectively. Given the clusterwise p-value, there is a corresponding critical cluster size. You can get this from a file in the QDEC output folder (in the contrast subfolder). The file will be called something like cache.th20.abs.pdf.dat. The 2nd column gives you the cluster size (in mm2) and the 4th column gives you the clusterwise p-value. Find the size of the cluster that corresponds to .05. In one data set I looked at, the size was about 328mm^2 doug Thanks in advance for the response. Binod ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ 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] RAS to Talairach
I am looking at intracranial electrode recordings from some epileptic patients. The locations of the electrodes have been determined using a preoperative MRI and a postoperative CT scan. The locations are in RAS coordinates. Is there some sort of function that will allow me to translate the RAS coordinates to Talairach coordiantes? Or some sort of function that will output an anatomical label for each of the RAS coordinates? Please let me know what I need in addition to the RAS coordinates as a .mat file. For example, do I need to install FreeSurfer? What additional files do I need? My preference would be to do this all in Matlab. Sincerely, Sujith ___ 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] few questions regarding qdec
Hi Du A.T. Brain 2007 ”Different regional patterns of cortical thinning in AD - used the smoothing level of 10-mm. This article can be added as reference. Additionally higher smoothing levels, for ex. at 20 mm, would bring partially inflated patterns due to excessive smoothing and due to failure of inference methods to control the proportion of false discoveries - Bernal-Rusiel, Neuroimage 2010 (www.ncibi.nlm.nih.gov/pubmed/20362677) while lower smoothing levels have an increased potential of preserving clusters with low significance. alex. Le 19/8 12:58, Douglas N Greve a écrit : On 08/16/2013 05:02 PM, Binod Thapa-Chhetry wrote: HI all, We had submitted a paper based on cortical thickness analysis in Qdec. The reviewer's had couple concerns regarding the QDec analysis. We would appreciate your help to address/resolve those issues. Here are the concerns: (1) What was the rationale of using 10mm smoothing? The typical fMRI values for volumteric work is 2-3 x the original voxel size. What's the reason for this value? Our response so far: A smoothing kernel of 10 mm was chosen because this setting had been published recently in articles that performed similar analyses. 10 mm therefore was a typical parameter for this type of analysis. This setting was also the default in the QDEC GUI, also suggesting that it was a typical setting. We only performed analyses of the data for this project using this setting and did not iteratively test multiple kernel widths. Also, the FWHM for cortical thickness analyses is somewhat larger than that used in fMRI analyses because it is applied to surface, as opposed to volume-based data. Surface based data are not prone to the same artifacts of including white matter, csf or brain tissue on the other side of a sulcus as volume-based data are. I think this is a good answer for a question that is not entirely fair. Aside from a few arguments about making GRF work, no one has ever had much of a justification for the particular choice of FWHM. It is just traditional at this point. You might point out that more smoothing is generally considered worse and that 10mm on the surface is much less than 10mm in the volume and people use 10mm in the volume is not unusual. (2) What's the p-value to get in for a cluster-wise analysis and what size is a significant cluster? It's important to know these non cluster-wise values to get a sense of the parameters that determine significance. Our response so far: QDEC does not have a parameter that can be adjusted for cluster size or extent as other whole brain analyses such as Statistical Parametric Mapping do. The researcher can only indicate a statistical cutoff. We used a p value cutoff of 0.05 after a correction for multiple comparisons that was based on the Monte Carlo permutation cluster analysis with 10,000 iterations. Additionally, our findings comprise of pretty large clusters. This obviates the reason for cluster-thresholding based on size. I'm not sure what the reviewer is asking. Is he/she asking for the cluster-forming, ie, voxel-wise, threshold? Or the p-value threshold for the cluster that you used to report clusters? You should report both. Both can be set in the QDEC GUI. I think the defaults are .01 and .05 respectively. Given the clusterwise p-value, there is a corresponding critical cluster size. You can get this from a file in the QDEC output folder (in the contrast subfolder). The file will be called something like cache.th20.abs.pdf.dat. The 2nd column gives you the cluster size (in mm2) and the 4th column gives you the clusterwise p-value. Find the size of the cluster that corresponds to .05. In one data set I looked at, the size was about 328mm^2 doug Thanks in advance for the response. Binod ___ 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.
Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt
Hi Francesco - There's a list of bedpostx output files here: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html The best way to determine if bedpostx finished running properly is to check if those files were created in the dmri.bedpostX directory. a.y On Mon, 19 Aug 2013, Francesco Siciliano wrote: Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory? ___ 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] RAS to Talairach
Hi Sujith, look at this page and see if it answers your questions http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug On 08/19/2013 01:23 PM, sujith vijayan wrote: I am looking at intracranial electrode recordings from some epileptic patients. The locations of the electrodes have been determined using a preoperative MRI and a postoperative CT scan. The locations are in RAS coordinates. Is there some sort of function that will allow me to translate the RAS coordinates to Talairach coordiantes? Or some sort of function that will output an anatomical label for each of the RAS coordinates? Please let me know what I need in addition to the RAS coordinates as a .mat file. For example, do I need to install FreeSurfer? What additional files do I need? My preference would be to do this all in Matlab. Sincerely, Sujith ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ 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] funcroi-table-sess error, set: Variable name must begin with a letter
Hi All, I'm trying to use funcroi-table-sess, but whenever I send this command: funcroi-table-sess -roi l_amyg_test -analysis habit_concat.mni305 -contrast neg1Vfix -sf subjects.lst -o l_amyg_neg1Vfix.dat I get this error: set: Variable name must begin with a letter So far as I can tell, all the variables in that command begin with a letter. Any idea what the problem might be? _ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _ ___ 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] trac-all inquiry
Hi Anastasia: I wish to echo David's sentiments. Thanks for this great software. I was able to process and extract data for all brains without losing any of the brains. Thanks so much. best, Alan On Fri, Aug 16, 2013 at 12:14 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Ok, actually the error about the data and bvals/bvecs not having the same size occured the first time you ran trac-all, but it seems to have been fixed the second time you ran it, based on the log file. I suspect the current problem is caused by poor registration. Have you checked the aparc+aseg and/or the registration from diffusion to anatomical and from anatomical to MNI? On Fri, 16 Aug 2013, David Soto wrote: hi - yes it as 65 -output pasted below, cheers dsoto@wmen-dsoto3:~/Documents/fmri/rsdtianawmgui/14AB/dmri$ mri_info dwi.nii.gz Volume information for dwi.nii.gz type: nii dimensions: 96 x 96 x 46 x 65 voxel sizes: 2., 2., 2.2999 type: FLOAT (3) fov: 224.000 dof: 0 xstart: -112.0, xend: 112.0 ystart: -112.0, yend: 112.0 zstart: -52.9, zend: 52.9 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 65 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0. : x_a = 0., y_a = 0.9774, z_a = -0.2112, c_a = 2.1015 : x_s = 0., y_s = 0.2112, z_s = 0.9774, c_s = 19.9194 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2. 0. 0. 112. 0. 2.2807 -0.4858 -96.1994 0. 0.4928 2.2480 -55.4405 0. 0. 0. 1. voxel-to-ras determinant -12.5217 ras to voxel transform: -0.4286 0. 0.48. -0. 0.4189 0.090545.3166 -0. -0.0918 0.425014.7274 0. 0. 0. 1. http://www1.imperial.ac.uk/medicine/people/d.soto/ On 16/08/13 16:13, Anastasia Yendiki wrote: mri_info dmri/dwi.nii.gz ___ 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] Curvature/folding stats
Hi all, What's the difference between the curvature and folding measures outputted in the aparc stats files (i.e. mean, gaussian, folding index, and curvature index)? Additionally, which measures are the most reliable for individual differences? Thanks, Mike Michael Kranz Graduate Research Assistant |Beckman Institute University of Illinois 314-323-1329 ___ 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] make_average_subject without aparc and talairach.xfm
Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html). I tried to download make_average_surface.no-aparc, however, the link seems to be broken. Also, I couldn't find a solution to the missing talairach.xfm on the list. It would be great if you could provide me with a working link to make_average_surface.no-aparc; any suggestions regarding making an average surface without talairach.xfm would be appreciated. I already made a new template and aligned all individual surfaces to this template. Thanks! Caspar ___ 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] segmentation fault - recon-all
Hello all, While running recon-all for a subject, I ran into the following error message: *reading aseg from /Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/aseg.auto_noCCseg.mgz* *reading norm from /Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/norm.mgz* *0 voxels in left wm, 0 in right wm, xrange [-1, 257]* *searching rotation angles z=[-7 7], y=[83 97]* *searching scale 1 Z rot 6.8 global minimum found at slice 0.0, rotations (90.00, -0.00)* *final transformation (x=0.0, yr=90.000, zr=-0.000):* *-0.000 0.000 1.000 128.000;* *-0.000 1.000 -0.000 128.000;* *-1.000 0.000 0.000 128.000;* * 0.000 0.000 0.000 1.000;* *Segmentation fault* *Darwin dhcp-165-124-23-248.prevmed.northwestern.edu 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64* *recon-all -s avgseg_seg_test exited with ERRORS at Mon Aug 19 13:32:28 CDT 2013* * * I don't know if this error is directly related to the actual brain segmentation, but recon-all was run with a different gca atlas. The command was: recon-all -gca atlas.gca -all -s subjID My best guess is that the .gca file is the source of the problem, but I am not sure why recon-all would make it to the final transformation and then throw an error. Any ideas? Thanks in advance. MP ___ 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] Curvature/folding stats
check out these links http://surfer.nmr.mgh.harvard.edu/fswiki/MeanCurvature http://surfer.nmr.mgh.harvard.edu/fswiki/GaussianCurvature On 08/19/2013 02:15 PM, Michael Kranz wrote: Hi all, What's the difference between the curvature and folding measures outputted in the aparc stats files (i.e. mean, gaussian, folding index, and curvature index)? Additionally, which measures are the most reliable for individual differences? Thanks, Mike Michael Kranz Graduate Research Assistant |Beckman Institute University of Illinois 314-323-1329 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ 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] make_average_subject without aparc and talairach.xfm
I've put that script here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html). I tried to download make_average_surface.no-aparc, however, the link seems to be broken. Also, I couldn't find a solution to the missing talairach.xfm on the list. It would be great if you could provide me with a working link to make_average_surface.no-aparc; any suggestions regarding making an average surface without talairach.xfm would be appreciated. I already made a new template and aligned all individual surfaces to this template. Thanks! Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ 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] make_average_subject without aparc and talairach.xfm
Hi Doug, that's great, thank you very much. From the previous posts I assume that this does not solve the issue with the missing Talairach.xfm. Do you have a recommendation for that? Thanks, Caspar 2013/8/19 Douglas N Greve gr...@nmr.mgh.harvard.edu I've put that script here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html). I tried to download make_average_surface.no-aparc, however, the link seems to be broken. Also, I couldn't find a solution to the missing talairach.xfm on the list. It would be great if you could provide me with a working link to make_average_surface.no-aparc; any suggestions regarding making an average surface without talairach.xfm would be appreciated. I already made a new template and aligned all individual surfaces to this template. Thanks! Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ 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.
Re: [Freesurfer] make_average_subject without aparc and talairach.xfm
I would probably just try to do it by hand. Copy a file with the identity matrix into the right folder, then run tkregister2 --fstal --s subject It will bring the human atlas up. I would then play with it a little bit to get it to look ok. For surface-based applications, it will have no effect on statistics, but it will affect the appearance of the pial and white surfaces (if you display your results on those instead of on the inflated). If you are not going to display on the white or the pial, then you can just leave it as the identity doug On 08/19/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, that's great, thank you very much. From the previous posts I assume that this does not solve the issue with the missing Talairach.xfm. Do you have a recommendation for that? Thanks, Caspar 2013/8/19 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu I've put that script here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html). I tried to download make_average_surface.no-aparc, however, the link seems to be broken. Also, I couldn't find a solution to the missing talairach.xfm on the list. It would be great if you could provide me with a working link to make_average_surface.no-aparc; any suggestions regarding making an average surface without talairach.xfm would be appreciated. I already made a new template and aligned all individual surfaces to this template. Thanks! Caspar ___ Freesurfer mailing list Freesurfer@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 gr...@nmr.mgh.harvard.edu mailto:gr...@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@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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] funcroi-table-sess error, set: Variable name must begin with a letter
Is there a folder called log in the directly you are running it from? If not, try creating one. If so, then run it with -debug as the first arg and send me the terminal output. doug On 08/19/2013 02:07 PM, Joseph Andreano wrote: Hi All, I'm trying to use funcroi-table-sess, but whenever I send this command: funcroi-table-sess -roi l_amyg_test -analysis habit_concat.mni305 -contrast neg1Vfix -sf subjects.lst -o l_amyg_neg1Vfix.dat I get this error: set: Variable name must begin with a letter So far as I can tell, all the variables in that command begin with a letter. Any idea what the problem might be? _ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ 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] fcseed-sess error
That looks good. Run these commands cd AC30_1319/Bold1/001 mri_label2vol --aparc+aseg --temp template.nii.gz --reg register.dof6.dat --o aparc+aseg.nii.gz mri_binarize --i aparc+aseg.nii.gz --match 4 --match 5 --match 43 --match 44 --match 31 --match 63 --count countfile.dat then send me the contents of countfile.dat doug On 08/19/2013 02:27 PM, Omar Singleton wrote: Sorry about that. I must have clicked 'reply' by mistake rather than 'reply all'. I wouldn't want to deprive anyone of the opportunity to help me resolve this issue. --The issue-- I looked at the segmentation in tkmedit and the labels for the ventricles showed up the same as in subjects that worked. I checked registration by eye and used this command from the tutorial: tkregister-sess -s AC30_1319 -fsd Bold1 -per-run -bbr-sum Which output: AC30_1319 001 0.4437 I'm not sure what the problem is with these subjects. Is there another way I should check the data? Any suggestions? -Omar Hi Omar, can you post questions to the list instead of us personally? thanks! doug On 08/19/2013 09:41 AM, Omar Singleton wrote: Hi Doug, Thanks for the help. I looked at the segmentation in tkmedit and the labels for the ventricles showed up the same as in subjects that worked. I checked registration by eye and used this command from the tutorial: tkregister-sess -s AC30_1319 -fsd Bold1 -per-run -bbr-sum Which output: AC30_1319 001 0.4437 I'm not sure what the problem is with these subjects. Is there another way I should check the data? Do you have any other suggestions? Best, Omar Hi Omar, it is not finding any ventricle voxels. Check the FS segmentation to make sure that the ventricles are labeled and also check the registration to make sure it looks ok. doug On 8/14/13 12:04 PM, O S wrote: Dear Support, I am trying to use fcseed-sess to create a ventricle and CSF regressor for my resting state analysis. I have encountered an error running fcseed-sess. fcseed-config -vcsf -fsd Bold1 -mean -cfg vcsf_bold1_config -overwrite works, but then the following command fails: fcseed-sess -s AC30_1319 -cfg vcsf_bold1_config -overwrite The above command worked for half my subjects and had the below error for half with no discernible pattern. I've run it on jizo as well as my home machine with the same error. Cut-and-paste the following info into your FreeSurfer problem report: - FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.4 (Final) Kernel info: Linux 2.6.32-358.2.1.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: jizo SUBJECTS_DIR: /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs PWD: /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs ssh jizo setenv SUBJECTS_DIR /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs - I would appreciate any help. Let me know if anything is unclear. Thank! Best, Omar Error Message * [jizo:fc_fs] (nmr-stable53-env) fcseed-sess -s AC30_1319 -cfg vcsf_bold1_config -overwrite Logfile is /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/log/fcseed-sess.vcsf_bold1_config.log.AC30_1319 Wed Aug 14 11:31:50 EDT 2013 Linux jizo 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs /usr/local/freesurfer/stable5_3_0/fsfast/bin/fcseed-sess -s AC30_1319 -cfg vcsf_bold1_config -overwrite freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Wed Aug 14 11:31:50 EDT 2013 Linux jizo 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs /usr/local/freesurfer/stable5_3_0/fsfast/bin/fcseed-sess -s AC30_1319 -cfg vcsf_bold1_config -overwrite freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 mri_label2vol --seg /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/mri/aparc+aseg.mgz --reg /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/register.dof6.dat --temp /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/template.nii.gz --fillthresh .95 --o /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz --pvf /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/pvf.nii.gz PVF
Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt
Hi Francesco - The bedpostx files are created when you run trac-all -bedp. Then you need to run trac-all -path to reconstruct the paths under dpath/... as the final step. Did you run this? a.y On Mon, 19 Aug 2013, Francesco Siciliano wrote: Thank you! Is it normal, however, not to have a dpath folder with summary statistics? I have all of the bedpostx output files, however, I seem to be missing the dpath folder as well as a script confirming that -path was completed. Thanks, Francesco From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Monday, August 19, 2013 1:56 PM To: Francesco Siciliano Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt Hi Francesco - There's a list of bedpostx output files here: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html The best way to determine if bedpostx finished running properly is to check if those files were created in the dmri.bedpostX directory. a.y On Mon, 19 Aug 2013, Francesco Siciliano wrote: Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory? 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] mergecontrasts-sess - Comparisons between subjects
Is it possible to do a conjunction analysis between subjects using one contrast? So far I've been able to do comparisons between contrasts within subjects but not between subjects. Thanks, -Ronny ___ 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] mergecontrasts-sess - Comparisons between subjects
Hi Ronny, you can use mri_concat with the --conjunction option, but I don't have a -sess command that does it doug On 08/19/2013 05:00 PM, preci...@nmr.mgh.harvard.edu wrote: Is it possible to do a conjunction analysis between subjects using one contrast? So far I've been able to do comparisons between contrasts within subjects but not between subjects. Thanks, -Ronny ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ 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] make_average_subject without aparc and talairach.xfm
Hi Doug, I ran make_average_surface.no-aparc and identity matrices on my data, and I seems to have completed the averaging without an error. However, when I try to view the result with tksurfer, I get an error because there is no average T1 for the average subject. How would you recommend I go about this? Do you have a make_average_volume.no-aparc as well, shall I make an average T1 manually, or can I skip the average T1? Thanks! Caspar 2013/8/19 Douglas N Greve gr...@nmr.mgh.harvard.edu I would probably just try to do it by hand. Copy a file with the identity matrix into the right folder, then run tkregister2 --fstal --s subject It will bring the human atlas up. I would then play with it a little bit to get it to look ok. For surface-based applications, it will have no effect on statistics, but it will affect the appearance of the pial and white surfaces (if you display your results on those instead of on the inflated). If you are not going to display on the white or the pial, then you can just leave it as the identity doug On 08/19/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, that's great, thank you very much. From the previous posts I assume that this does not solve the issue with the missing Talairach.xfm. Do you have a recommendation for that? Thanks, Caspar 2013/8/19 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu I've put that script here ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/make_average_surface.no-**aparcftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before (http://www.mail-archive.com/**freesur...@nmr.mgh.harvard.** edu/msg15595.htmlhttp://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html ). I tried to download make_average_surface.no-aparc, however, the link seems to be broken. Also, I couldn't find a solution to the missing talairach.xfm on the list. It would be great if you could provide me with a working link to make_average_surface.no-aparc; any suggestions regarding making an average surface without talairach.xfm would be appreciated. I already made a new template and aligned all individual surfaces to this template. Thanks! Caspar __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number:
[Freesurfer] Fwd: calloc error
i have tried running the centos 4 6 versions of freesurfer on ubuntu 12.04, and with either i am getting a memory error when i simply run mri_info on an mgz file (this does not happen on my osx machine for the same file , and the license file is fine): znzTAGskip: tag=1667787808, failed to calloc 606085120 bytes! Cannot allocate memory any help would be appreciated. cheers, @rno ___ 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] make_average_subject without aparc and talairach.xfm
You can just copy in the T1.mgz from fsaverage (won't matter that it is human), or you can try running make_average_volume to make a NHP volume. Not sure that will work, but make sure to use --no-aseg doug On 8/19/13 8:43 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I ran make_average_surface.no-aparc and identity matrices on my data, and I seems to have completed the averaging without an error. However, when I try to view the result with tksurfer, I get an error because there is no average T1 for the average subject. How would you recommend I go about this? Do you have a make_average_volume.no-aparc as well, shall I make an average T1 manually, or can I skip the average T1? Thanks! Caspar 2013/8/19 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu I would probably just try to do it by hand. Copy a file with the identity matrix into the right folder, then run tkregister2 --fstal --s subject It will bring the human atlas up. I would then play with it a little bit to get it to look ok. For surface-based applications, it will have no effect on statistics, but it will affect the appearance of the pial and white surfaces (if you display your results on those instead of on the inflated). If you are not going to display on the white or the pial, then you can just leave it as the identity doug On 08/19/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, that's great, thank you very much. From the previous posts I assume that this does not solve the issue with the missing Talairach.xfm. Do you have a recommendation for that? Thanks, Caspar 2013/8/19 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu I've put that script here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html). I tried to download make_average_surface.no-aparc, however, the link seems to be broken. Also, I couldn't find a solution to the missing talairach.xfm on the list. It would be great if you could provide me with a working link to make_average_surface.no-aparc; any suggestions regarding making an average surface without talairach.xfm would be appreciated. I already made a new template and aligned all individual surfaces to this template. Thanks! Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://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 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@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@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
