Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Qdec question
by Devdutta W 13 Feb '09

13 Feb '09

Hi, I have been running into an error while using Qdec. *Error in Analyze: Couldn't open file <$SUBJECT_DIR>/<SUBJECT_FOLDER>/surf/lh.thickness.fwhm10.fsaverage.mgh* I checked and the file is there in that folder. I know this file is created when recon-all is run with -qcache option. I have run that twice and it still gives me the same error. What could be going wrong here and how can I fix it? Thanks, Dev

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Cannot allocate memory
by Jürgen Hänggi 13 Feb '09

13 Feb '09

Dear FS experts I tried to make an average subject of 52 subjects, but it seems that an already fixed error is back: Checking 47 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po laris_Male_48.mgh Checking 48 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po laris_Male_49.mgh Checking 49 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po laris_Male_50.mgh Checking 50 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po laris_Male_51.mgh Checking 51 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po laris_Male_52.mgh nframestot = 52 Allocing output MRIalloc(256, 256, 256): could not allocate 262144 bytes for 11862th slice Cannot allocate memory ERROR: make_average_volume [Neuropsycho@130 subjects]$ I had the same problem with an older Mac FS version. Is there also a fixed version of FS 4.2.0 for Linux CENTOS 32 bit? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) 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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eTIV
by Gabriel Go.Es. 13 Feb '09

13 Feb '09

Dear freesurfers: I have two questions: 1. I have FS v4.0.5 and i've downloaded the new mri_segstats to calculate the eTIV, this new calculation may cause any trouble in my group of manual segmented subjects? 2. I have 60 subjects manual segmentated on FreeSrufer 4.0.5, i want to know if i run the recon2 or recon3 in the new FS 4.2.0, will have any problem? the diferences between versions can cause any trouble with the analisis because imcompability or something? Regards Gabriel ¿Tu fondo de escritorio es aburrido? Anímalo con las imágenes más espectaculares _________________________________________________________________ Consigue gratis el nuevo Messenger. ¡Descárgatelo! http://download.live.com/

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13 Feb '09

Dear all, I would like to automatically corregister PET to MRI by using the command bbregister. I am not sure what is going on since Freesurfer (release 4.0.5) always says "Command not found" when I try to run this function. Any help with this issue would be very welcome. Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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new eTIV calculation
by Nick Schmansky 13 Feb '09

13 Feb '09

If you make use of the estimated Total Intracranial Volume (eTIV) calculation found in the aseg.stats file of your subject data, then you should be aware that we have recently found a more accurate way to make this calculation. We have found that using the talairach.xfm transform instead of the talairach_with_skull.lta transform, from which the determinant is extracted and multiplied by a scale factor, results in lower variability of the eTIV calc in our test set. This new way of calculating eTIV will appear in the next release of Freesurfer. If you want to make use of this new calculation right away, you can download a new version of mri_segstats from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes and run it using this command: mri_segstats --subject subjid --etiv-only and it will output the new eTIV. Nick

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eTIV
by Gabriel Go.Es. 13 Feb '09

13 Feb '09

Dear freesurfers: I have 60 subjects manual segmentated on FreeSrufer 4.0.5, i want to know if i run the recon2 or recon3 in the new FS 4.2.0, will have any problem? the diferences between versions can cause any trouble with the analisis because imcompability or something? Regards Gabriel _________________________________________________________________ Llévate Messenger en tu móvil allá donde vayas ¿A qué esperas? http://serviciosmoviles.es.msn.com/

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pial and white matter surface areas
by Al-Radaideh Ali 12 Feb '09

12 Feb '09

Dear FreeSurfer Expert, I am trying to find the surface areas of Pial surface and white matter surface. I found many files in Surf folder but not sure which is which and how t read them in a text, Excel,or matlab file. any idea please? The other thing, If I have many subjects, is there any way I can read the surface areas in a table or any text file as well. I use this command asegstats2table to group the volumes of specific structures in one table. Thanks in advance Ali 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.

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RE: White matter defect
by karlkarl 12 Feb '09

12 Feb '09

Hello, I sending in two more sagigital views. You mentioned it was related to the aseg. In the tutorial exmaples of defects, it always uses brainmask as a guide to fix the problem in wm.mgz, which wouldn't work in this case. Would you give some intrctions on corrction from aseg. thanks > Date: Thu, 5 Feb 2009 16:48:48 -0500 > From: fischl(a)nmr.mgh.harvard.edu > To: rememberer(a)hotmail.com > Subject: RE: [Freesurfer] white matter defect > CC: freesurfer(a)nmr.mgh.harvard.edu > > I see. The ventricles are filled in from the aseg, but if you filled in > the wm.mgz that would work as well. It may not be needed though. What does > it look like in a saggital view? > _________________________________________________________________ 新版手机MSN，满足你多彩需求！参加抢鲜体验活动，领取特色奖品！ http://mobile.msn.com.cn/

3 3

topological defect
by Dankner, Nathan (NIH/NIMH) [F] 11 Feb '09

11 Feb '09

Hello, In many of the surfaces that I have made, a frequent error seems to center around the ventricles. The white matter segmentation often does not follow the white matter near the ventricle, leaving a circle inside the ventricle area. This seems to create a dimple on the output surface. I have attached a screenshot of the surface (the dimple is obvious) and also of a coronal and saggital slice of the wm.mgz where the error occurs. How is this best fixed? Thanks, Nathan

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exited with errors
by Dankner, Nathan (NIH/NIMH) [F] 11 Feb '09

11 Feb '09

Hello all, I have recently been running some scans with very few defects, but have been encountering a particular error message on occasion when I try to run it through autorecon2 and autorecon3 after a bit of manual correction. The error output is: MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory Any suggestions as to why this is happening? Nathan

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