Freesurfer

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30091 discussions

Downsampling/decimating overlays (not surfaces)
by Nicola Toschi 24 Jan '13

24 Jan '13

Hello list, is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100. Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward). Thanks a lot in advance, Nicola PS apologies for the repost - my subject line was incorrect the first time around.

4 5

mni152reg error (file permission denied)
by raij＠nmr.mgh.harvard.edu 23 Jan '13

23 Jan '13

Dear Surfers, mni152reg --$SUBJECT exits with the error: mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402': Permission denied Thereafter, a couple consequential errors follow ... niiWrite(): error opening file /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii ... ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii This is on FS 5.1.0 stable. The error seems linux box independent. Please let me know if you need further info. Thanks! Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Results Vary
by Varghese Chikku 23 Jan '13

23 Jan '13

Dear FS team, I processed two set of MRI data for a single patient,Thats BL scan and TP1.I ran both scans on a Mcbook Pro and a PC with Virtual machine installed. Though I was expecting the same segstats,the results vary from Macpro to VM.For eg , for BL in Mac SubCortGrayVol is 178038 but for the same images in VM the results are 177432.Does it happened to any one before....Whats the reson its happening and how can I remedy,validate the results. Much appreciate your advice,... In Thanks Chikku.

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Empty search space
by Jürgen Hänggi 23 Jan '13

23 Jan '13

Dear FS experts I run a longitudinal analysis, and all steps (cross, base, long) were run without errors. I used QA tools in order to look at the results and all recons are fine. However, when running glmfit with the --osgm option there is no error message, but there is also no results (sig=0, F=0). In the log I realized that the mask is empty (see below). Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to Cap_Thickness_LH.glmdir/mask.mgh Reshaping mriglm->mask... search space = 0.000000 What are the most plausible reasons for this empty mask? Should I try the pruning option? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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tracula bedpostx failure
by Cat Chong 22 Jan '13

22 Jan '13

Hello Experts, I am running bedpost x through fsl on the dmri directory (as advised in a previous post). I receive the fsl error message: “child process exited abnormally”. The command line error states: switching from /8000_tracula/8000_tracula_out/8005_DTI/dmri to /8000_tracula/8000_tracula_out/8005_DTI bedpostx /8000_tracula/8000_tracula_out/8005_DTI/dmri -n 2 -w 1 -b 1000 /Applications/fsl/bin/bedpostx /8000_tracula/8000_tracula_out/8005_DTI/dmri -n 2 -w 1 -b 1000 subjectdir is /8000_tracula/8000_tracula_out/8005_DTI/dmri /8000_tracula/8000_tracula_out/8005_DTI/dmri/data not found All the output files of the trac-all -prep stage are there, but could I have made a mistake on my configuration file? I have attached it. Thank you very much for your help, Cheers, Cat

2 1

question about persession versus perrun motion correction
by Maryam Vaziri Pashkam 22 Jan '13

22 Jan '13

Hi Dough, This might be a very basic question: I would like to compare the results of an analysis with the perrun and persession motion correction. Here is my analysis line: *mkanalysis-sess \* * -analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt \* * -native -mcextreg -stc siemens -fwhm 0 \* * -event-related -paradigm para_cat.par -nconditions 5 \* * -spmhrf 0 -TR 2 -refeventdur 4 -polyfit 2* * * * * * And here is what I have in my analysis info analysis Cat_1 mcstem fmc fsd bold runlistfile run_1.txt TR 2 RegDOF 6 RawSpace volume native mask brain RawFWHM 0 RawSTC siemens UseB0DC 0 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 5 parname para_cat.par RefEventDur 3 timewindow 40.000000 prestim 0 TER 0.050000 spmhrf 0 stimulusdelay -1.00000000000000000000 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 nuisreg mcextreg 3 I preprocessed my data once using the perrun option and once using the persession option in two different directories and ran the analysis on both of those data sets. The problem is when the analysis finished the results where practically identical. I am not sure what is going on and can't figure out if the analysis in both cases is done based on the persession motion correction or they are both done based on the perrun motion correction and how I can get the analysis to run in two different ways. I am using freesurfer 5.1. M *

2 3

Downsampling/decimating overlays (not surfaces)
by Nicola Toschi 22 Jan '13

22 Jan '13

1 0

freesurfer@nmr.mgh.harvard.edu
by Nicola Toschi 22 Jan '13

22 Jan '13

1 0

Re: [Freesurfer] question about persession versus perrun motion correction
by Douglas N Greve 22 Jan '13

22 Jan '13

Oh, right, I remember now (at least mostly). I fixed that for version 5.2. Maryam, it may be that the code is not actually using the persession data like it should. doug On 01/22/2013 03:19 PM, raij(a)nmr.mgh.harvard.edu wrote: > Hi Doug, > > There at least used to be a bug in the way perrun/persession was handled. > We exchanged emails about that about a years ago (see especially Tapsya's > emails). If I recall correctly we were never able to make this work > without rigging the file extensions etc (FS-FAST always defaulted to one > stream and/or one file extension regardless of which option was used). Not > sure if this is still a problem, but could be related to Maryam's email. > > Cheers, > > Tommi > > >> Hi Maryam, when you say that they are practically identical, I assume >> that there are at least some small differences indicating that something >> was different? And what are you comparing exactly? Eg, single subject or >> group? In principle, they should be pretty close to each other, it >> depends entirely on how much the subject moved between runs and how much >> smoothing you apply. If you have a well-behaved population, then there >> might not be much of a difference. If you reduce the smoothing to 0, >> then you might start to see more of an effect. >> >> doug >> >> >> On 01/22/2013 02:44 PM, Maryam Vaziri Pashkam wrote: >>> Hi Dough, >>> >>> This might be a very basic question: >>> I would like to compare the results of an analysis with the perrun and >>> persession motion correction. Here is my analysis line: >>> >>> >>> *mkanalysis-sess \* >>> >>> *-analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt \* >>> >>> *-native -mcextreg -stc siemens -fwhm 0 \* >>> >>> *-event-related -paradigm para_cat.par -nconditions 5 \* >>> >>> *-spmhrf 0 -TR 2 -refeventdur 4 -polyfit 2* >>> >>> * >>> * >>> * >>> * >>> * >>> And here is what I have in my analysis info >>> >>> analysis Cat_1 >>> mcstem fmc >>> fsd bold >>> runlistfile run_1.txt >>> TR 2 >>> RegDOF 6 >>> RawSpace volume native >>> mask brain >>> RawFWHM 0 >>> RawSTC siemens >>> UseB0DC 0 >>> inorm 100 >>> acfbins 30 >>> fixacf 1 >>> acffwhm 20 >>> acfsvd 0 >>> designtype event-related >>> nskip 0 >>> polyfit 2 >>> HPFCutoffHz 0 >>> HeteroGCor 0 >>> nconditions 5 >>> parname para_cat.par >>> RefEventDur 3 >>> timewindow 40.000000 >>> prestim 0 >>> TER 0.050000 >>> spmhrf 0 >>> stimulusdelay -1.00000000000000000000 >>> Condition 1 Condition01 >>> Condition 2 Condition02 >>> Condition 3 Condition03 >>> Condition 4 Condition04 >>> Condition 5 Condition05 >>> nuisreg mcextreg 3 >>> >>> >>> >>> I preprocessed my data once using the perrun option and once using the >>> persession option in two different directories and ran the analysis on >>> both of those data sets. The problem is when the analysis finished the >>> results where practically identical. I am not sure what is going on >>> and can't figure out if the analysis in both cases is done based on >>> the persession motion correction or they are both done based on the >>> perrun motion correction and how I can get the analysis to run in two >>> different ways. I am using freesurfer 5.1. >>> >>> M >>> * >> -- >> 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: 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 >> >> >> > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] long_mris_slopes / mris_calc problem
by O'Shea,Andrew 22 Jan '13

22 Jan '13

I was able to solve my problem in my earlier email included below. I downloaded a new verison of mris_calc made it executable with chmod +x FILE and then replaced it in the bin folder. I included this response in case anyone else runs into the same problem and does a search. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-int… ---- Hello Freesurfer experts, I am working on a study that wants to compare pre/post cortical thickness on an intervention group and a control group. I am using FS 5.1 on a Mac. I have processed all the recons through the longitudinal stream as described in the wiki/tutorial. However when I go to prepare the data using this command: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage It seems to run fine at first but after a minute or so it hits this command and crashes: mris_calc -o /Applications/freesurfer/subjects/SPIN073/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-SPIN073_lh_thickness_igG3e9/beta1.mgh div ./tmp-SPIN073_lh_thickness_igG3e9/beta0.mgh It prints: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? And then returns to my command prompt. I searched online and found someone last year asked the same question here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-September/02031… However the response links to an updated version of mris_calc but when I click the link it says I do not have permission the access. Thanks for any help in advance. -Andrew

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