Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

recon-all error
by Anil Roy 09 Oct '06

09 Oct '06

Hello all, I get the following error when I feed in a dicom file into recon-all. The dicom file is in a directory with 159 other dcm files. Can you please tell me how to rectify this or what the source of the error is. [root@dhcp-129-105-146-217 freesurfer]# recon-all -i /root/Cath/ADULT\ 14-0005-0001-0001.dcm -subjid E001 -sd /usr/local/freesurfer/subjects -all set: Variable name must begin with a letter. Thanks, Anil.

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about ROI
by Lei.Zhang＠uniklinik-freiburg.de 09 Oct '06

09 Oct '06

Hi, Dear FreeSurfers, I'm using FreeSurfer and successfully overlaid the functional activations onto the flatten surface. Now I want to isolate the functional area as ROI and get its average of the amplitude and percent of signal changes in different tasks. I looked up the helpful information in the handbook and Tutorial, but still no ideas. I hopelly someone can give me a guidance about this. Any hints would be appreciated! Thanks, Lei

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corrupted curvature file
by Balaji Lakshmanan 04 Oct '06

04 Oct '06

Dear all, One of our subjects have a corrupted curvature file(lh.curv) due to some overwriting. This subject was reconstructed using older version of freesurfer. I would like to know which step/command should I rerun in order to retrieve this file. Thanks in advance, Balaji

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roisummary and FIR
by Cameron Ellis 04 Oct '06

04 Oct '06

Hi, I am running roisummary with an FIR analysis with a 25s timewindow, 5s prestim and TR=2.5s. I In the summary output I receive 10 nestpercond but shouldn't I receive 11 with these parameters? timecourse: -5.0 -2.5 0.0 2.5 5.0 7.5 10.0 12.5 15.0 17.5 20.0 timepoint: 0 1 2 3 4 5 6 7 8 9 10 I did not mask the roi. If I should only receive 10 nestpercond which timepoint is left out? Thanks in advance. Cameron

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functional overlay onto the occiptal patch with fieldsign
by Lei.Zhang＠uniklinik-freiburg.de 04 Oct '06

04 Oct '06

Hi Dear FreeSurfers, I'm using the new version of FreeSurfer to process retinotopic data. I can view the finial results of eccen, polar and fieldsign on the occiptal patch. Now I want to overlay another block designed activations onto the fieldsign patch with file---load overlay--select the corresponding fsig_000.bfloat---select register.dat---OK, but actually no activations appeared on the patch altough the fsig_000.bfloat can be shown on the overlay layer. Would smeone let me know how to overlay the functional activations onto the retinotopic patch? Thanks in advance! Lei

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Converting DICOMs
by Fornito, Alexander 04 Oct '06

04 Oct '06

Hi, I'm new to fMR and am using mri_convert to convert from siemens dicom to analyze/spm format.I ran the command below and had a couple of questions: 1 - Why does the first INFO: line say that 807 files were found when only 805 were input? 2 - Why were only 800 of 805 files converted? 3 - As it says at the end of the output, the axial plane is flipped. Is there any way I can prevent this? Thanks for your help, Alex mri_convert -it siemens_dicom 21851740 -ot spm ../test mri_convert -it siemens_dicom 21851740 -ot spm ../test reading from 21851740... Getting Series No Scanning Directory INFO: Found 807 files in /data/flanders/work/alex/freesurfer/subjects_pace/epi_test/04271947 INFO: Scanning for Series Number 2 INFO: found 800 files in series INFO: loading series header info. INFO: sorting. RunNo = 1 INFO: ( 64 60 21), nframes = 800, ismosaic=1 Numaris Version: syngo MR 2004V 4VB11D Maj = 4, Min=1, MinMin = 1 Computing TR with number of slices Repetition Time = 1420, TR = 29820 ms FileName /data/flanders/work/alex/freesurfer/subjects_pace/epi_test/04271947/21851800 Identification NumarisVer syngo MR 2004V 4VB11D ScannerModel Avanto PatientName Fornito^Alex^^^Mr Date and time StudyDate 20060427 StudyTime 192350.703000 SeriesTime 192556.781000 AcqTime 192554.055005 Acquisition parameters PulseSeq epfid2d1_60 Protocol ep2d_800 PhEncDir COL EchoNo 0 FlipAngle 78 EchoTime 26 InversionTime 26 RepetitionTime 1420 PhEncFOV 206.25 ReadoutFOV 220 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 300 NImageCols 320 NFrames 800 SliceArraylSize 21 IsMosaic 1 ImgPos 106.2426 139.4769 -20.2630 VolRes 3.4375 3.4375 5.0000 VolDim 64 60 21 Vc -0.9981 -0.0053 0.0606 Vr 0.0000 -0.9962 -0.0873 Vs 0.0608 -0.0872 0.9943 VolCenter -0.3610 31.5859 29.5993 TransferSyntaxUID 1.2.840.10008.1.2.1 should never get here INFO: no Siemens slice order reversal detected (good!). TR=29820.00, TE=26.00, TI=26.00, flip angle=78.00 i_ras = (-0.998149, -0.00531035, 0.0605839) j_ras = (3.3967e-08, -0.996181, -0.0873174) k_ras = (0.0608162, -0.0871557, 0.994337) writing to ../test... Analyze Output Matrix -3.431 0.000 0.304 109.370; -0.018 -3.424 -0.436 143.355; 0.208 -0.300 4.972 -25.143; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' ... Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito(a)wh.org.au

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is there any online resource for manual segmentations of subcortical objects...
by Shahabuddin Ansari 03 Oct '06

03 Oct '06

Hello, Is there any online resource for manual segmentations of subcorical objects, e.g. hippocampus, amygdala, caudate etc? I appreciate it. Shahab --------------------------------- Stay in the know. Pulse on the new Yahoo.com. Check it out.

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Missing Dicom Fields (Revisted)
by Niels Bergsland 03 Oct '06

03 Oct '06

Hi again, >From the last time that I asked about this, the project was temporarily put on hold, but now it has started up again... When looking back at the responses from last time, I realized that I am not sure if I made it clear what I was proposing as a solution to the missing fields 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). My original question was as follows: Is it possible to 'fake' the 20,37 field by inserting the values: 1\0\0\0\1\0 since we know they are acquired in the axial plane? We also know which way the slices are supposed to be sorted, is it possible to insert values into 20,32 in order to have freesurfer able to 'know' the proper sorting order? To which you said that you didn't have something to allow us to specify the fields ourselves. I realized that you thought I was asking if Freesurfer has the capability. What I actually meant though is if I can manually insert the values using, for example, dcmodify (part of the DCMTK) and then process the scans with Freesurfer. Hopefully this is a bit more clear! Thanks again, Niels Bergsland

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flattened but two surfaces
by Joongnam Yang 03 Oct '06

03 Oct '06

Hi all, I flattened the occipital cortex and viewed it with tksurfer, but there are two flattened surfaces, top and bottom on the tksurfer window. Usually from my experience, there is one flattened surface. Could someone suggest what might have gone wrong? Nam.

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Re: [Freesurfer] mris_flatten missing 4 lib
by Joongnam Yang 03 Oct '06

03 Oct '06

Dear all, I did occipital cortex flattening and when I tried to display it on tksurfer using "tksurfer average lh occip.patch.flat", I got the following error message, which I have never seen. (the error message on memory) surfer: current subjects dir: /home/nam/AVERAGE surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/nam/AVERAGE/average/surf Loading tal xfm file /home/nam/AVERAGE/average/mri/transforms/talairach.xfm surfer: Reading header info from /home/nam/AVERAGE/average/mri/T1.mgz MRISalloc(16711682, 408): could not allocate vertices Cannot allocate memory Would someone hint at a solution? Nam.

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