Freesurfer September 2010

freesurfer@nmr.mgh.harvard.edu

93 participants
127 discussions

Re: [Freesurfer] control points
by Ali Radaideh 07 Sep '10

07 Sep '10

Hi Bruce, Catting the file shows something like cat control.dat info numpoints 0 useRealRAS 0 The version of freesurfer is freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Unfortunately, I repeated hat you suggested in your previous email (-make all) to another subject but failed at some point although this subject's data have been proceed month ago successfully ( the data from the first subject still running), the error is: second estimation of the COG coord: x=129,y=120, z=120, r=9758 iterations GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 22554 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1548 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 1656 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=33 , nb = 9459 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 9819 OTHER CSF_MIN=0, CSF_intensity=18, CSF_MAX=39 , nb = 72 mri_watershed Error: GLOBAL region of the brain empty ! Linux comp13 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC x86_64 x86_64 x86_64 GNU/Linu x recon-all exited with ERRORS at Mon Sep 6 15:03:10 BST 2010 Thanks Ali -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, September 06, 2010 3:30 PM To: Ali Radaideh Subject: RE: [Freesurfer] control points Hi Ali, can you post your responses to the list? Try catting that file to see what's in it. Also, what version are you running? cheers Bruce On Mon, 6 Sep 2010, Ali Radaideh wrote: > Hi Bruce, > > control.dat file is there (size=75). > > Actually I finished running this subject before and checked that. > > Now I am running the recon-all with -make all flag as you suggested and > it is working fine. > > But not sure if 'reading 0 control points' means that there will be no > improvement after running the recon-all !! > > Thanks > Ali > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Monday, September 06, 2010 2:03 PM > To: Ali Radaideh > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] control points > > Hi Ali, > > the control points are saved in the subject's directory under > > <subject id>/tmp/control.dat > > does that file exist? It also looks like you hadn't finished running > this > subject previously. Try running -make all in recon-alll which will rerun > > only what it needs to. > > cheers > Bruce > > > On Mon, 6 Sep > 2010, Ali Radaideh wrote: > >> Dear Freesurfer experts, >> >> >> >> One more question for today please. I have edited the wm in tkmedit > and >> saved the control points then ran >> >> >> >> Recon-all -autorecon2-cp -autorecon3 -s mySubjectName >> >> >> >> But unfortunately I got the following message after 5min of running. I >> tried to use a different subject but I got the same message again. >> >> >> >> It was displaying a message that it is 'reading 0 control points'. Is >> this message related to the error below? >> >> >> >> mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta >> -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz >> >> >> >> logging cutting plane coordinates to ../scripts/ponscc.cut.log... >> >> INFO: Using transforms/talairach.lta and its offset for Talairach > volume >> ... >> >> using segmentation aseg.auto_noCCseg.mgz... >> >> reading input volume...done. >> >> searching for cutting planes...voxel to talairach voxel transform >> >> 1.047 0.006 0.067 -14.718; >> >> 0.005 1.161 0.015 -27.233; >> >> -0.083 -0.006 1.022 -2.059; >> >> 0.000 0.000 0.000 1.000; >> >> mri_fill: could not read segmentation from aseg.auto_noCCseg.mgz >> >> reading segmented volume aseg.auto_noCCseg.mgz... >> >> ERROR: cannot find >> /data_local/ali/freesurfer/subjects/ali1/mri/aseg.auto_noCCseg.mgz >> >> No such file or directory >> >> Linux comp07 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC > x86_64 >> x86_64 x86_64 GNU /Linux >> >> >> >> recon-all exited with ERRORS at Mon Sep 6 13:00:12 BST 2010 >> >> >> >> >> >> >> >> Many thanks >> >> Ali >> >> 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. > _______________________________________________ > 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. > > > >

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selxavg3-sess on OSX
by Jason Webster 06 Sep '10

06 Sep '10

I'm running v5.0 on 10.6.4. When I run selxavg3-sess, I get the following error: > > ERROR: cannot determine format of /Users/jwebst/UW/Psych/VisCog/projects/vAttPRF/data/vAttPilot01/bold/003/masks/brain.nii.self.lh ERROR: cannot load /Users/jwebst/UW/Psych/VisCog/projects/vAttPRF/data/vAttPilot01/bold/003/masks/brain.nii.self.lh I'm not familiar with the creation of the maskfspec field or of flacfiles generally. Is it the case that there is a flacfile for each analysis (so the correct mask is brain.self.lh.nii)? ...or should it be loading brain.nii and '.self.lh' was erroneously appended? Also, one tangential issue worth mentioning for the release August 16 release for Intel OSX... it seemed to be missing 3dvolreg. ~Jason

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mri_robust_register
by j janssen 06 Sep '10

06 Sep '10

Hi, - using version 4.5 in the v4.5 standard longitudinal processing stream with 2 images mri_robust_register creates halfway space transformations using the 2 time point's norm.mgz files. i would like to apply the halfway transformations (mri_convert -at) to the 2 time point's _original_ (001.mgz) images. can i do this and if so, how? or should i create new halfway transformations with something like: mri_robust_register --mov timepoint1_001.mgz --dst timepoint2_001.mgz --lta v1to2.lta --halfmov h1.mgz --halfdst h2.mgz --halfmovlta h1.lta --halfdstlta h2.lta --iscale thanks, -joost

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control points
by Ali Radaideh 06 Sep '10

06 Sep '10

Dear Freesurfer experts, One more question for today please. I have edited the wm in tkmedit and saved the control points then ran Recon-all -autorecon2-cp -autorecon3 -s mySubjectName But unfortunately I got the following message after 5min of running. I tried to use a different subject but I got the same message again. It was displaying a message that it is 'reading 0 control points'. Is this message related to the error below? mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.047 0.006 0.067 -14.718; 0.005 1.161 0.015 -27.233; -0.083 -0.006 1.022 -2.059; 0.000 0.000 0.000 1.000; mri_fill: could not read segmentation from aseg.auto_noCCseg.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find /data_local/ali/freesurfer/subjects/ali1/mri/aseg.auto_noCCseg.mgz No such file or directory Linux comp07 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC x86_64 x86_64 x86_64 GNU /Linux recon-all exited with ERRORS at Mon Sep 6 13:00:12 BST 2010 Many thanks Ali 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.

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Volumes/Areas
by Jose Soares 06 Sep '10

06 Sep '10

Hi all freesurfers, What volume/area should I use to measure the motor cortex? Is there a way to measure the volume/area of medial or ventromedial prefrontal cortex? Thanks for the help, Jose.

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cortical volume
by Ali Radaideh 06 Sep '10

06 Sep '10

Hello, After the success of running the freesurfer on the 7T human data a while ago, I am trying now to extract the cortical volume. However, if I use asegstats2table command to get the segmented volume then I get the following values Rt_cerebral_cortex = 236732 Lt_cerebral cortex = 242649 While if I use the read_curv in Matlab I get the following values Rt_cerebral_cortex = 209050 Lt_cerebral cortex = 208080 Any reasons for such difference, please? As I need also to normalise these values to the intracranial volume ICV, do you think it is better then to use the asegstats2table command as it lists the ICV in its outputs as well? Many thanks in advance Ali 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.

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I/O performance mitigation
by David Mischel 03 Sep '10

03 Sep '10

We took the suggestion of staggering the launch of Freesurfer 5.0 recon-all jobs. The attached Word doc (I don't know how to contribute this information other than attaching the image and text using Word) shows a load graph on our file server. When 20 FS jobs began at once (all processing servers using a single file server) the load on the file server bulged up. When we spaced out the launch of each job by 15 seconds the load hardly budged. We have not had to do this in the past with earlier versions of Freesurfer but this is an obvious work around to the problem we encountered. < david David Mischel Manager of IT Center for Imaging of Neurodegenerative Diseases (CIND) <http://www.cind.research.va.gov/> http://www.cind.research.va.gov/ VA Medical Center 4150 Clement Street, 114M San Francisco, CA 94121 voice: 415-221-4810 x3864 fax: 415-668-2864

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reading PET in Matlab
by Rafa x 03 Sep '10

03 Sep '10

Dear Freesurfers, I’m trying to obtain in matlab the PET value of each vertex of the cortex from one freesurfer subject. To calculate it, first I do the coregister with: bbregister -–mov PETimage.nii –-t2 –-s subjectName –-init-fsl –-reg register.dat I have checked the result and it is provides perfect corregister between the PET and MRI. Then I calculate the PET in the cortical surface with: mri_vol2surf -–mov PETimage.nii –-reg register.dat –-hemi ?h –projfrac 0.5 –-interp nearest –-o PETSurface.mgh I load it with tksurfer like an overlay. It shows the variability of the PET activity across the cortex without problem. At last I extract the parameters in Matlab with: [vol, M, mr_parms, volsz]=load_mgh(PETSurface.mgh) The problem appears when I compare the values of PET in some vertices. The most of the vertices checked (not all) doesn’t have the same value in tksurfer and matlab (obtained with vol(numberOfVertex)). The values in tksurfer and matlab are similar (in the same magnitude order) but are not equal. Maybe I’m taking a wrong way of obtain the PET activity in Matlab. I hope that someone can help me. Thank you all in advance, Rafael.

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Re: [Freesurfer] OSX bug in getrunlist
by Douglas N Greve 03 Sep '10

03 Sep '10

Yes, you are correct! I've put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/getrunlist copy it into $FREESURFER_HOME/fsfast/bin doug Jason Webster wrote: > Hey Doug, > > I am just trying out 5.0 on OSX and stumbled into a bug in getrunlist. > > The command: > set RunList = (`find -maxdepth 1 -name "[0-9][0-9][0-9]"`); > needs to be replaced with: > set RunList = (`find . -maxdepth 1 -name "[0-9][0-9][0-9]"`); > lest it throws: > > find: illegal option -- - > find: illegal option -- m > find: illegal option -- a > find: illegal option -- e > find: illegal option -- p > find: illegal option -- t > find: illegal option -- h > find: 1: No such file or directory > > > > ~Jason > -- 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

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Re: [Freesurfer] Talairach afd error
by Oya, Hiroyuki 03 Sep '10

03 Sep '10

talairach.xfm file is as below: ---------------------- MNI Transform File % tkregister2 Transform_Type = Linear; Linear_Transform = 1.37266099 0.20895453 0.18430687 13.98477840 0.46526164 0.99459654 -3.29530478 68.71842194 -0.81687593 0.73364604 3.47314310 -136.09573364 ; ------------------------ This looks awful. an image is also attached. Thanks again. On Fri, 2010-09-03 at 09:36 -0400, Bruce Fischl wrote: > can you post these to the list so others can answer? Did you check the > talairach.xfm with either tkmedit or tkregister2? > > On Fri, 3 Sep 2010, Oya, Hiroyuki wrote: > > > Hi Bruce, > > > > Bringing up the image with tkmedit, directions are correct. > > And I have not done any process in Analyze format. > > > > Thank you. > > > > > > > > > > > > On Fri, 2010-09-03 at 09:24 -0400, Bruce Fischl wrote: > > > >> Hi Hiroyuki, > >> > >> can you check to make sure that the direction cosines are correct? Bring up > >> the orig.mgz and make sure that coronal is coronal, sagittal is sagittal > >> and horizontal is horizontal. Did this data go through analyze at any time? > >> > >> cheers > >> Bruce > >> > >> > >> On Fri, 3 Sep 2010, Oya, Hiroyuki wrote: > >> > >>> Dear all, > >>> > >>> > >>> recon-all failed at the talairach stage. > >>> > >>> > >>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > >>> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > >>> Linux hiroyuki-desktop 2.6.32-24-generic #42-Ubuntu SMP Fri Aug 20 > >>> 14:21:58 UTC 2010 x86_64 GNU/Linux > >>> > >>> > >>> In what circumstances do we see this? > >>> T1 STRUCTURAL looks OK . Any comment would be appreciated. > >>> > >>> Hiroyuki > >>> > >>> > >>> > >>> > >>> > >> > >> > >> 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. > >> > > > > > > //***********************// > > Hiroyuki Oya, M.D. > > Assistant Professor, > > Department of Neurosurgery, > > University of Iowa, > > 200 Hawkins drive, Iowa City, > > IA, 52242-1061, USA > > tel:1-319-353-8452 > > e-mail: hiroyuki-oya(a)uiowa.edu > > fax:1-319-353-6605 > > > > > > //***********************// Hiroyuki Oya, M.D. Assistant Professor, Department of Neurosurgery, University of Iowa, 200 Hawkins drive, Iowa City, IA, 52242-1061, USA tel:1-319-353-8452 e-mail: hiroyuki-oya(a)uiowa.edu fax:1-319-353-6605

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Freesurfer September 2010