Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

unable to download data from wiki page
by Alexander Lebedev 08 Jan '11

08 Jan '11

Dear Freesurfer users, Sorry for disturbing... I've got some problems with FS after updating my workstation (segfault error). Before reporting a bug I decided to try to reinstall FS. But for some reasons I can't download any data from wiki page: looks like server is closed... I need freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.0.0/freesurfer-Linux…] Would you be so kind to provide me any other links to this archive? Thank you beforehand. -- Best Regards, Alexander Lebedev, I.P. Pavlov State Medical University, 197022, Lev Tolstoy str. 6/8, Saint Petersburg, Russian Federation. tel.:+7-921-441-79-42 e-mail: awlman(a)rambler.ru Skype ID: celtic__frost -- Твой город, улица и дом на http://maps.rambler.ru

3 2

label2label error
by Lena Palaniyappan 07 Jan '11

07 Jan '11

For some of my data, label2label (one of the PALS labels from fsaverage being mapped on to a subject) gives this message Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table Is there anything I can do to circumvent this? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

3 3

using mri_glmfit-sim; precached or not
by Chris Hyatt 07 Jan '11

07 Jan '11

Dear Freesurfer users, I am using mri_glmfit-sim to do clusterwise correction for multiple comparisons. I ran the Z Monte Carlo simulation for 5000 iterations for my 43 subjects (vertex wise threshold of 2.0 or p < 0.01), but I received different results than when I ran the correction using the "new" pre-cached simulation (using threshold of 2.0). In general, I get fewer clusters when running the simulation from scratch when compared with the pre-cached simulation. I used the fsaverage subject brain in the original analysis. Here are the commands I ran: initial glmfit (uncorrected): mri_glmfit --y lh.HCvsCD.thickness.10.mgh --fsgd HCvsCD.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.HCvsCD.glmdir Then corrections for multiple comparisons .... from scratch: mri_glmfit-sim --glmdir lh.HCvsCD.glmdir --sim mc-z 5000 2.0 mc-z.pos --sim-sign pos --bg 5 using pre-cached: mri_glmfit-sim --glmdir lh.HCvsCD.glmdir --cache 2.0 pos Which method is most accurate? Also, how does one turn off the polling writes to the console when running MC-Z from scratch? Thanks, Christopher Hyatt Olin Neuropsychiatric Research Center / IOL Hartford, CT

2 1

monkey surface
by Christidis, Patricia P. (NIH/NIMH) [C] 07 Jan '11

07 Jan '11

Hello, I'm trying to make a surface for a monkey volume that is 256 by 296 by 256 voxels in size. I know that if I use recon-all -autorecon, I can add the -cw256 flag to deal with that FOV of 296. But with a monkey volume, my understanding is that I can't use recon-all. Instead, I need to use the older programs like mri_convert, correct? If so, how do I deal with a FOV greater than 296? Thank you Peggy Christidis

1 0

Qdec and 3 groups GLM
by Lena Palaniyappan 07 Jan '11

07 Jan '11

I have a single factor with three levels (diagnosis) and trying to setup qdec, but I get the following message - I have a .levels file with all 3 groups specified - the contrasts are not getting generated automatically. Data table loading completed successfully. SUBJECTS_DIR is '/Volumes/FREECOM/Applications/freesurfer/subjects/conn' ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 87 Checking inputs nframestot = 87 Allocing output Done allocing nframes = 87 Writing to /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/y.mgh gdfReadHeader: reading /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/qdec.fsgd INFO: gd2mtx_method is dods Reading source surface /Volumes/FREECOM/Applications/freesurfer/subjects/conn/fsaverage/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/y.mgh --fsgd /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/qdec.fsgd dods --glmdir /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled --surf fsaverage lh --label /Volumes/FREECOM/Applications/freesurfer/subjects/conn/fsaverage/label/lh.aparc.label Any help? Thanks Lena ________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

2 1

variance or stdev from average
by Thesen, Thomas 07 Jan '11

07 Jan '11

Hi, I am using mris_average_curvature to create an average thickness map across subjects (registered to fsaverage). The command line I am running is: mris_average_curvature lh.thickness lh sphere.reg subj01 subj02 .... subj20 outputfile This produces the average, but my question is if there a way to also create a measure of variability at the vertex level from that group, e.g. the associated variance or standard deviation? Thanks, Thomas </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE>

3 2

mkanalysis-sess and -TER
by Yuko Yotsumoto 07 Jan '11

07 Jan '11

Hi all, (-------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 --------) I created sequences for event-related design, using optseq2. optseq2 --ntp 150 --tr 2 --psdwin 0 20 1 --ev TG1 2 22 --ev IG1 2 22 --ev CNT 2 22 --ev TGIG 2 22 --ev TGCN 2 22 --nsearch 2000 --focb nCB10pt --nkeep 15 --o MO Then, I did: preproc-sess -df sessdirfile -s MO01B -fwhm 5 -fsd bold mkanalysis-sess -analysis fmcsm5TER1 -TR 2 -paradigm para.para -designtype event-related -funcstem fmcsm5 -motioncor -runlistfile runfile6 -inorm -polyfit 2 -mcextreg -nconditions 5 -timewindow 20 -prestim 4 -TER 1 -autostimdur -force mkcontrast-sess -analysis fmcsm5TER1 -contrast AllNull -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 selxavg3-sess -s MO01B -df sessdirfile -analysis fmcsm5TER1 -overwrite -TER in mkanalysis-sess doesn't seem to be working correct (see the right picture in the link). when I set -TER for mkanalysis-sess to be 2, the plot looks fine (see the left picture in the link). http://www.nmr.mgh.harvard.edu/~yuko/images/HDR_TER2_TER1.jpg Does this mean the sequence I used wasn't good for -TER=1? Or is there a way to make the plot right? Yuko

2 1

ICV and adjusting watershed
by L.Hoekstra＠psy.umcn.nl 07 Jan '11

07 Jan '11

Dear Freesurfer users, We were suprised to find out in two cases that after adjusting watershed (because of skull that was left) and autorecon2 and autorecon3, the ICV was exactly the same as the ICV measured by pipeline--> autorecon-all. If we didn't adjust watershed in one case the skull was included in the pial. Did we had to rerun autorecon 1 after adjusting watershed to get the skull out of the ICV measure? thx, Liesbeth Hoekstra Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

2 1

.label file for each ROI?
by Ingalhalikar, Madhura 06 Jan '11

06 Jan '11

Hi, I am trying to implement FSL and freesurfer to compute structural adjacency matrix. The webpage http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html has been a major help. I just have one question. When I use probtrackx for fiber tracking, I have to seed the cortical ROI's and subcortical structres one by one. In this case, how can I create a .label file for each cortical and subcortical ROI;s ? Thanks for your help, Madhura The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

2 3

black background to white in tksurfer
by Ritobrato Datta 06 Jan '11

06 Jan '11

Is there a way to set the black background to white in tksurfer ? Thanks Ri

1 0

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