Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

trac-all download
by ana ;osp 14 Aug '13

14 Aug '13

hi'm trying to download the trac-all file from the site in the tracula release notes, it is the download from 2012/1/09 recommended for all, but hen i click it open a page and gives me an error should i do something different than just click? thanks

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FS version
by Cristian Paz 14 Aug '13

14 Aug '13

Dear experts! I have a question. I have run recon-all on a cluster , and I am editing on my local machine. I just checked the versions and I see that I have: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522 at the computing cluster and freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on my local computer.... Is this a problem? Thank you very much for your help. Kind regards Cris

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".thickness.fwhm15.fsaverage.mgh" missing
by Muhammad Naveed Iqbal Qureshi 14 Aug '13

14 Aug '13

Dear List Members, I converted my data from .dcm to .nii and than from .nii to .mgz volume, after that I have run the following command to calculate the cortical thickness; recon-all -s sub01 -all but I have not get ".thickness.fwhm15.fsaverage.mgh" files in the surf folder after recon-all get finished without errors. Please tell me the reason of the absence of these files. Previously I did not converted my data to .nii and I got all the files in surf folder. I used the following command earlier recon-all -i <path-to-dicom> -subject <name-of-the-subject> -all -qcache & waiting for reply Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to

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Prevent masking of activity outside of brain
by Cesar Echavarria 14 Aug '13

14 Aug '13

Hi Freesurfers, I want to look at activity in my subjects' retina for one of my experiments. I did volume-based analysis in freesurfer version 5.3 but I noticed that activity outside of the brain has been masked. Is there an option somewhere along the processing pipeline to prevent masking of activity outside the brain? I know that freesurfer version 4.5 does not do this masking, but was wondering if there was a way to stick to the current freesurfer version. Thanks you in advance for your help. Cesar

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Fwd: Unsegmented ventricles
by Victor Kovac 13 Aug '13

13 Aug '13

Hi Bruce, I have never used expert options in Freesurfer. I googled "freesurfer expert options" and this link came up ( http://ftp.nmr.mgh.harvard.edu/fswiki/recon-all#Arguments) but I do not see how to specify ranges. Is it a flag after recon-all? Could you show me an example of how to set gm T1.mgz values? Thank you very much! Victor On Tue, Aug 13, 2013 at 3:55 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Victor > > yes, look at the expert options. You can set the range of allowable wm and > gm values (and csf for that matter). > > cheers > Bruce > > On Tue, 13 Aug 2013, Victor Kovac wrote: > > Hi Bruce, >> I was using v5.1 but switched to v5.3 for these troublesome cases. The >> biggest issue is that this is a longitudinal study and these scans are >> from >> patients' 4th visits. Looking in the asegstats tables from all 4 visits, >> it >> would appear that the patients having this issue have had a ~20% increase >> in >> cortical WM since their 3rd visit last year, after showing a steady >> decline >> previously. >> >> There isn't great GM/WM contrast, so I added control points to this >> subject. >> That reset the T1.mgz value of voxels that I would consider to be WM to >> 109 >> or higher, yet I still see nearly all GM with T1.mgz values in the 80's >> and >> 90's segmented as WM, which is why I am confused. >> >> From what I can see, for this brain (MPS3008-4) only voxels with a T1.mgz >> of >> less than 80 are being segmented as GM. Is there a way for me to manually >> plug in the voxel intensity ranges for GM and WM and re-create the >> surfaces? >> >> Thank you very much for your help with this! >> >> Victor >> >> On Tue, Aug 13, 2013 at 3:29 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > >> wrote: >> never mind, I see the problem. I think this is due to the lack >> of gray/white contrast in this subject. I'll try some control >> points, but it may be that it will need some expert opts to >> specify the white and pial intensity ranges >> On Mon, 12 Aug 2013, Victor Kovac wrote: >> >> Dear Bruce, >> I have uploaded the subject with unsegmented >> ventricles (MPS3025-4) via File >> Drop. This subject has an artifact from a >> ventricular shunt in his left >> hemisphere, and we are only using data from his >> right hemisphere. >> >> I have also uploaded a subject (image attached) >> whose cortical GM is being >> segmented as WM, and whose pial boundary is extended >> past the cortex. This >> is a recurrent issue with the atrophied brains I am >> working with. I added >> control points to bright white matter voxels in >> order to re-threshold WM >> voxel intensity and hoped that re-running >> autorecon-cp -autorecon3 would fix >> the issue, but it seems to have done nothing. >> >> Could you take a look at this subject and tell me if >> you know there is a way >> to get FreeSurfer to take my re-thresholding >> attempts and recreate the pial >> and white matter boundaries? >> >> Please let me know if there was an issue with my >> upload, and, again, thank >> you for your help! >> >> Victor >> >> On Fri, Aug 9, 2013 at 2:28 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> hmmm, you could manually correct it but if you >> upload that >> dataset I'll take a look as well >> >> >> On Fri, 9 Aug 2013, Victor Kovac wrote: >> >> Dear Bruce, >> As I have been looking through brains I >> have run >> recon-all on with v5.3, I'm >> noticing that there are many cases of >> lateral >> ventricles being left >> unsegmented in subjects with dilated >> ventricles. >> >> An image of one case of unsegmented >> ventricles is >> attached, where a subject >> has an artifact from his shunt which may >> be causing >> the error. I have >> manually adjusted this subject's >> talairach to fix >> its talairach failure. >> Should I be using the attached script >> "tkmedit-lv.sh" to fill the >> ventricles, or is there a better method? >> >> Thank you very much for your help. >> >> Victor >> >> On Fri, Aug 2, 2013 at 1:13 PM, Bruce >> Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Victor, >> >> yes, 5.3 is most of what you need. >> I think I >> added a couple of >> control points as well, but they >> should be in >> the subject dir i >> sent you. >> >> cheers >> Bruce >> On Fri, 2 Aug 2013, Victor Kovac >> wrote: >> >> Bruce, >> Thank you so much for >> analyzing this >> subject -- the >> segmentation looks much >> better! Was it simply >> running the >> subject with v5.3, >> or did you add any >> flags to the recon? >> >> As you mentioned, the pial >> and white >> matter surfaces >> extend further than >> they should, but I have >> found adding >> control points >> to white matter near the >> cortical surface has helped >> a lot in >> similar cases. >> >> I have two other subjects >> whose >> ventricles were left >> unsegmented, but have >> less atrophy than the >> subject I sent >> you. I tried >> filling the ventricles >> using the attached script, >> then ran >> recon with >> -autorecon2-wm -autorecon3 >> flags, but it did not have >> any effect. >> Would you >> recommend just running the >> subject with v5.3? >> >> Thank you! >> >> Victor >> >> On Thu, Aug 1, 2013 at 10:32 >> AM, Bruce >> Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Victor >> >> the 5.3 recon finished >> and you can >> grab the >> subject from: >> >> >> >> >> http://gate.nmr.mgh.harvard.**edu/filedrop2/?p=if8d3r4<http://gate.nmr.mgh.harvard.edu/filedrop2/?p=if8d3r4> >> >> I think the ventricles >> are *much* >> better. The >> white surface was >> incorrect in anterior >> temporal >> regions due to >> lack of >> myelination, but that >> is expected. >> You might >> be able to improve >> them, but there is >> little enough >> contrast that >> I'm not sure how >> good they will be >> >> cheers >> Bruce >> >> >> >> On Tue, 30 Jul 2013, >> Victor Kovac >> wrote: >> >> Dear Freesurfer >> experts, >> I am running recon-all >> on very >> atrophied >> brains with mixed >> results. Attached >> is an image of a brain >> where >> segmentation has >> gone awry. >> There is no message >> indicating talairach >> failure, and >> the >> segmentation appears >> to need WM and >> pial edits as well as >> the >> ventricles to be >> filled, so I am >> not sure how to >> proceed. >> >> If you have any >> recommendations as >> to how to >> fix these >> errors, I would very >> much appreciate it -- >> these data >> are past >> their deadline, >> and I am at a >> loss. >> >> Thank you! >> >> Sincerely, >> Victor >> >> >> >> >> 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<http://www.partners.org/complianceline>. >> If the >> e-mail was sent to you >> in error >> but does not contain patient >> information, please >> contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> >> >> >> >> >> >>

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optseq2
by Claire Wilcox 13 Aug '13

13 Aug '13

hello, i'm struggling with how to specify a schedule and then ask optseq2 to identify an optimal timing schedule. specifically i have a conditioned cue and an unconditioned stimulus. the high threat CS always needs to follow with a high pain US and low threat CS with a low pain CS. how can i specify such a schedule in optseq2? i've been trying a number of combinations of below, but am failing miserably with lots of varying warnings and error messages and inability to read files or 'Bus error' what should the --in input schedule file format look like? that might be the missing link .. although that's hard to say for sure. many thanks, claire

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Re: [Freesurfer] QDEC error in asegstats2table
by Douglas N Greve 13 Aug '13

13 Aug '13

Hi Ken, I cannot reproduce this error, and I can't find anything wrong with the file you sent. If you remove this subject, does the process complete? doug On 08/09/2013 10:58 AM, Rando, Kenneth wrote: > Hi Doug, > > Thanks for having a look at these files. The first attached file, from Subject_Dir tb0294, is the file previous to the file with the error, tb0314, attached second. > > Ken > > > Kenneth Rando > Research Assistant 2 > 203-974-7731 > > Yale OCD Research Clinic > Yale University School of Medicine > Connecticut Mental Health Center > 34 Park Street, Room W309 > New Haven, CT 06519 > > > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Thursday, August 08, 2013 5:23 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] QDEC error in asegstats2table > > Ken, can you send the offending file and the file from the 6th subject? > doug > > On 08/08/2013 03:09 PM, Rando, Kenneth wrote: >> Hello Experts, >> >> This QDEC error is one that appears in the archives, but I did not see >> a solution that solves my problem. The error (after some information >> about initialization of the program) is as follows: >> >> >> SUBJECTS_DIR : /home/freesurfer_ocd >> Parsing the .stats files >> ERROR: The stats file /home/freesurfer_ocd/tb0314 /stats/aseg.stats is >> not found or is too small to be a valid statsfile >> Use --skip flag to automatically skip bad stats files >> ERROR: In >> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, >> line 230 >> vtkKWQdecApp (0x27a1f070): >> Script: >> vtkTemp2 GenerateStatsDataTables >> Returned Error on line 1: >> Uncaught exception: command failed: asegstats2table --common-segs >> --meas volume --tablefile >> /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat >> --statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 >> tb0294 tb0314 tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 >> tb0892 tb0901 tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 >> tb2073 tr7582 tr7733 tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 >> tr8285 tr8345 tr8511 tr8529 tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 >> tr9222 tr9332 tr9459 tr9515 tr9561 tr9707 tr9746 tr9765 tr9824 >> >> Stack trace: >> Uncaught exception: command failed: asegstats2table --common-segs >> --meas volume --tablefile >> /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat >> --statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 >> tb0294 tb0314 tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 >> tb0892 tb0901 tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 >> tb2073 tr7582 tr7733 tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 >> tr8285 tr8345 tr8511 tr8529 tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 >> tr9222 tr9332 tr9459 tr9515 tr9561 tr9707 tr9746 tr9765 tr9824 >> >> while executing >> "vtkTemp2 GenerateStatsDataTables" >> >> The error occurs at the seventh subject in the dataset, so it appears >> to be subject-specific. As recommended in previous posts, I have >> verified that the aseg.stats file exists for that subject. I am new to >> Freesurfer, but a comparison of this aseg.stats file to the previous >> subject's file and a few others reveals no obvious differences (e.g., >> missing lines, extreme or corrupt data values). >> >> One response to an earlier post asked the user to run asegstats2table >> -i aseg.stats -t test.dat in the stats directory of the file with the >> error. I followed that advice and it produces a file for this subject. >> There was, however, no follow-up posting, so I don't know what that >> indicates, and how I should follow-up. >> >> Thanks for your help. >> >> Ken >> >> >> >> Kenneth Rando >> Research Assistant 2 >> 203-974-7731 >> >> Yale OCD Research Clinic >> Yale University School of Medicine >> Connecticut Mental Health Center >> 34 Park Street, Room W309 >> New Haven, CT 06519 >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > 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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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mri_glmfit covariates
by Rees, Elin 13 Aug '13

13 Aug '13

Hi, I'm trying to run a cortical thickness group comparison (HD v Controls), controlling for site, gender (1 or 2) and age. Without age as a covariate the results are as expected but once age is added on all significant results disappear. I think this is a problem with the method rather than because all results are dependent on age. My fsgd and contrast files for the glm are below. I would really appreciate your input as to what might be going wrong to effect the results so strongly. Am I doing something wrong? GroupDescriptorFile 1 Title HDvControl Class HD-london-1 Class HD-leiden-1 Class HD-paris-1 Class HD-ulm-1 Class HD-london-2 Class HD-leiden-2 Class HD-paris-2 Class HD-ulm-2 Class C-london-1 Class C-leiden-1 Class C-paris-1 Class C-ulm-1 Class C-london-2 Class C-leiden-2 Class C-paris-2 Class C-ulm-2 Variables Age Input 30009 HD-paris-2 26 Input 30014 C-ulm-2 51 Input 30016 C-london-1 48 Input 30024 C-leiden-1 38 Input 30029 HD-london-2 66 Input 30030 HD-london-1 54 Input 30037 HD-london-2 42 Input 30041 C-london-1 43 Input 30042 HD-london-2 40 Input 30043 HD-london-2 41 Input 30047 HD-london-2 66 Input 30051 C-london-2 45 Input 30054 HD-london-2 55 Input 30056 C-london-2 66 Input 30060 C-london-1 50 Input 30068 C-london-1 51 Input 30071 HD-london-1 43 Input 30072 HD-london-2 44 Input 30074 C-london-2 58 Input 30075 HD-london-2 48 Input 30078 C-london-2 53 Input 30079 HD-london-1 58 Input 30082 C-london-2 62 Input 30089 HD-london-2 54 Input 30093 HD-leiden-1 44 Input 30098 HD-leiden-2 45 Input 30100 HD-leiden-2 42 Input 30102 C-leiden-2 48 Input 30107 HD-leiden-2 61 Input 30112 HD-leiden-2 50 Input 30114 C-leiden-1 48 Input 30115 HD-leiden-2 47 Input 30117 HD-leiden-2 49 Input 30118 C-leiden-1 51 Input 30119 HD-leiden-2 59 Input 30124 C-leiden-1 57 Input 30125 HD-leiden-2 39 Input 30136 C-leiden-2 51 Input 30138 C-leiden-2 56 Input 30139 HD-leiden-2 33 Input 30142 HD-leiden-2 32 Input 30148 HD-leiden-1 48 Input 30154 C-leiden-1 47 Input 30155 HD-leiden-2 46 Input 30160 HD-leiden-2 38 Input 30162 HD-leiden-2 52 Input 30163 C-leiden-2 42 Input 30168 C-ulm-2 58 Input 30177 C-london-2 49 Input 30185 C-ulm-2 34 Input 30189 HD-ulm-1 50 Input 30191 C-ulm-1 44 Input 30193 HD-ulm-1 46 Input 30195 C-ulm-2 50 Input 30198 C-ulm-1 56 Input 30199 HD-ulm-1 53 Input 30208 HD-ulm-1 59 Input 30209 C-ulm-2 44 Input 30210 HD-ulm-1 30 Input 30214 HD-ulm-2 57 Input 30215 HD-ulm-1 34 Input 30220 HD-ulm-2 54 Input 30222 HD-ulm-1 64 Input 30223 C-ulm-1 44 Input 30229 HD-ulm-1 40 Input 30235 HD-ulm-1 48 Input 30240 HD-ulm-1 36 Input 30241 C-paris-2 65 Input 30247 HD-paris-1 24 Input 30248 HD-paris-1 44 Input 30250 HD-paris-2 62 Input 30254 HD-paris-1 37 Input 30256 HD-paris-1 23 Input 30259 HD-paris-1 64 Input 30265 C-paris-2 50 Input 30269 C-paris-2 58 Input 30273 C-paris-2 49 Input 30275 C-paris-1 59 Input 30280 HD-london-2 42 Input 30281 HD-london-2 65 Input 30288 HD-london-2 51 Input 30311 HD-paris-1 40 Input 30312 HD-paris-2 51 Input 30314 HD-paris-2 46 Input 30315 HD-leiden-2 67 Input 30318 C-paris-2 64 Input 30320 C-paris-1 49 Input 30321 HD-paris-1 61 Input 30326 C-paris-2 45 Input 30334 HD-london-1 49 Input 30347 C-paris-1 62 Input 30349 HD-paris-2 48 Input 30352 C-paris-2 66 Input 30357 C-ulm-1 28 Input 30361 HD-paris-2 63 Input 30363 HD-ulm-1 51 Input 30365 C-ulm-2 46 Input 30369 HD-ulm-2 45 Input 30378 C-leiden-1 53 Input 30385 HD-leiden-2 61 Input 30392 HD-ulm-2 51 Contrast: 1 1 1 1 1 1 1 1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Thanks, Elin

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hippocampal segmentation converting mgz to nii
by lorenzo pasquini 13 Aug '13

13 Aug '13

Dear freesurfer users, I have used freesurfer to segment hippocampal subfields. Then I used freeview to convert the derived .mgz files in .nii files for further analysis. I estimated the hippocampal subfields volumes with the command: kvlQuantifyPosteriorProbabilityImages $ FREESURFER_HOME/ data/ GEMS/ compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz I have calculated the number of voxels in the converted .nii files using SPM and realized that they do not fit the estimated volumes through freesurfer Example for CA2-2 estimated voxel number though freesurfer: 6851 voxels found in .nii file: 15812 Did somebody had similar problems? Do you have any suggestion? Are there any incompatibilities between SPM and freesurfer? I did not find any apparent error in my counting script. Thank you very much and regards, Lorenzo Pasquini Can. Ph. D., Medical Life Science and Technology (Technische Universität Muenchen) Neuroimaging Lab, Neuroradiology Klinikum r. d. Isar (Technische Universität) 81675 München Tel.: 0049 (0) 89 4140-7666

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Error when using preproc-sess -per-session in FS-5.3
by Sepide Movaghati 13 Aug '13

13 Aug '13

Hello, I am using freesurfer 5.3 and try to run: preproc-sess -s session1 -surface self lhrh -fsd bold -mni305 -fwhm 5 -per-session it gives me an error: 1/1 session1 1/1 session1 003 lh --------- Mon Aug 12 11:21:09 EDT 2013 ERROR: could not determine file for /export01/data/sepid/subjects/ZY/session1/bold/003/fmcpr however, it works fine when I use -per-run. I have attached complete terminal output. Thanks.

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