Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Best way to convert Philips par/rec to mgz
by Julie McEntee 18 Nov '09

18 Nov '09

Hello, I have T1-weighted data from Philips 3 T scanner obtained at a resolution of 0.898 X 0.898 X 0.9 mm in both dicom (8 bit) and par/rec (pixel size = int16) format. I would like to preserve the acquisition resolution of the data in par/rec format; what is the best way to convert such data to mgz format for analysis in freesurfer? A command line example would be helpful, as I am new to freesurfer. Thanks for your help, Julie Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676

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recon without normalization
by africa millan 18 Nov '09

18 Nov '09

Hello, When I run the function recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization I've got an ERROR message: Skull Stripping /root/trabajo/freesurfer/subjects/c1prueba/mri mri_watershed -T1 -brain_atlas /root/trabajo/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C ERROR: cannot find /root/trabajo/freesurfer/subjects/c1prueba/mri/T1.mgz mri_watershed Error: read failed Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Nov 18 11:05:17 CET 2009 When I open de mri file of the subject, I realize that there is not any T1.mgz file, because freesurfer did not generate it. So the question is, when I run the function recon-all with the -nonormalization flag added, does freesurfer skip the generation of the T1.mgz file? Thanks for your help, Africa. > Date: Tue, 17 Nov 2009 13:25:56 -0500 > From: sita(a)nmr.mgh.harvard.edu > To: africa_millan(a)hotmail.es > Subject: RE: [Freesurfer] recon without normalization > > > > Yes, that looks okay. You can also add -autorecon3 flag if you want the > dataset to go through the whole recon-all stream. > > Thanks, > Sita. > > > > On Tue, 17 Nov 2009, africa millan wrote: > > > > > Hello Sita, > > > > > > > > Is this the right way to add the -nonormalization flag to the recon-all function to skip the normalization step during the first recon-all??: > > > > > > > > "recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization " > > > > > > > > > > > > Thanks for your help! > > > > > > > > Africa. > > > > > > > > > > > > > > > >> Date: Thu, 12 Nov 2009 13:24:54 -0500 > >> From: sita(a)nmr.mgh.harvard.edu > >> To: africa_millan(a)hotmail.es > >> CC: freesurfer(a)nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] recon without normalization > >> > >> > >> > >> You can run recon-all with -nonormalization flag, which will skip that > >> step. > >> > >> Sita. > >> > >> > >> > >> On Thu, 12 Nov 2009, africa millan wrote: > >> > >>> > >>> Hello, > >>> > >>> > >>> > >>> Another question:If during the first recon-all, freesurfer makes skullstripping and normalization automatically... Is there any way to run the first recon-all without automatic normalization? > >>> > >>> > >>> > >>> Is it possible? > >>> > >>> > >>> > >>> Thanks > >>> > >>> Af. > >>> > >>> _________________________________________________________________ > >>> Descubre todas las formas en que puedes estar en contacto con amigos y familiares. > >>> http://www.microsoft.com/windows/windowslive/default.aspx > > > > _________________________________________________________________ > > Sólo hay un loro experto en Windows 7 en todo el mundo. Y vive en Sietes ¡Cónocelo! > > http://www.sietesunpueblodeexpertos.com/ 49 habitantes, 49 expertos en Windows 7. Así es Sietes, ¡Visítalo! _________________________________________________________________ Deja que Sietes te enseñe todo los secretos de Windows http://www.sietesunpueblodeexpertos.com/

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Qdec table
by Dankner, Nathan (NIH/NIMH) [F] 18 Nov '09

18 Nov '09

Hi all, I am attempting to create a qdec.table.dat file, and have been unable to find a way to paste my data into it in a way that will make it readable. When I paste it in qdec always outputs an error when trying to open it, even if visually the file appears to be correct. Is there an easy way to import data from excel into something readable by qdec? I'm hoping to avoid having to manually enter everything because there is quite a lot of data, so any help would be appreciated. Thanks, Nathan

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slopes of interaction analysis in tksurfer
by Stefan Brauns 17 Nov '09

17 Nov '09

Hi all, I have done an analysis of thickness and a neuropsych variable as a covariate with mri glmfit. I would now like to see the neuropsych slopes of different groups (patients vs. controls) for certain vertices in tksurfer. After loading the sig.mgh overlay and the corresponding file descriptor file, I can only view at the intercepts (see picture). Is there a possibilty to show the slopes as well ? Furthermore the picture only shows 12 groups, although I have actually 16 and I don't know why. Many thanks, Stefan -- Stefan Brauns 15 Clark St Boston, MA, 02109 phone: (617) 398-0437

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ICV for incomplete whole brain coverage
by Juranek, Jenifer 17 Nov '09

17 Nov '09

A colleague asked me to look at some T1s for possible Freesurfer analyses. Unfortunately, several subjects do not have whole brain acquisitions (I know, quite unexpected and disappointing). Would it be possible to correct volumes of subcortical structures (which are covered by the acquisition) for ICV in the absence of whole brain coverage? The T1s were acquired in the coronal plane...so typically brain tissue is missing in either the anterior and/or posterior regions. I reflexively think that whole brain coverage is required for accurate ICV calculated by Freesurfer...but I'm not positive. Many Thanks for any thoughts you might have, Jenifer

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recon - local directory
by Rajagopalan, Venkateswaran 17 Nov '09

17 Nov '09

Dear Freesurfer users, I don't have privileges to create directories in freesurfer installation folder as i am using freesurfer from server. So i am not able to run "recon-all -s Desktop/test/sub1/vol1.mgz -autorecon1" giving a path name to a folder in Desktop where my image volume is stored. So how to run this command. Thanks in advance. venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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edits to pial surface
by Dana W. Moore 17 Nov '09

17 Nov '09

Hi everyone, I have an image in which the pial surface left out portions of the cortex (see left temporal lobe below). I am not sure how to go about editing this. I tried adding control points to the brainmask.mgz volume and running -autorecon2-cp -autorecon3, but the result seems unchanged (see control points in picture below). Did I do something wrong? The edit voxels tool I believe would help if the problem was that these voxels had been removed during skull-stripping, but this is not the case--they were just excluded from the pial boundary. Thanks, Dana Emacs! Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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Average brain error
by Anna Rotarska-Jagiela 17 Nov '09

17 Nov '09

Dear Freesurfer Users, during the creation of average brain with Freesurfer, I got the following ERROR message: > > getpwdcmd: command not found > > ERROR: format for rh.orig.avg.area.mgh not recognized. > > ERROR: make_average_surface do you have any idea what this might be? The Freesurfer version I'm using is 4.4.0. I also attach the log file. I would appreciate your help. Sincerely, Anna Rotarska-Jagiela -- ------ Dr. Anna Rotarska-Jagiela Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt a.M. Germany Email: rotarska(a)mpih-frankfurt.mpg.de Phone: +49 69 6301 83782 Fax: +49 69 6301 3833 ------ http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm ------

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tkmedit
by Rajagopalan, Venkateswaran 17 Nov '09

17 Nov '09

Hello, I am new to freesurfer, i having the following problem. I placed my subject's data in folder "Desktop/test/sub1/vol1.mgz". I used "tkmedit sub1 vol1 -f $bme/home..Desktop/test" the following command to open and view my image and i get the following error " bme undefined variable. What is the mistake i am doing here. How can i access the folders created in Desktop since i don't have privileges to create or access folders in Freesurfer directory as my freesurfer runs from the server. Thanks venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Clusterwise Correction for Multiple Comparisons error
by Weisinger, Brian (NIH/OD) [E] 17 Nov '09

17 Nov '09

I am trying to do the clusterwise correction for multiple comparisons and came upon a problem that maybe someone can help me with. ri_volcluster --in brianweisinger/g1g2.intercept/sig.mgh --csd brianweisinger/csd/mc-z.negative.j001-g1g2.intercept.csd --mask brianweisinger/mask.mgh --cwsig brianweisinger/g1g2.intercept/mc-z.negative.sig.cluster.mgh --vwsig brianweisinger/g1g2.intercept/mc-z.negative.sig.voxel.mgh --sum brianweisinger/g1g2.intercept/mc-z.negative.sig.cluster.summary --ocn brianweisinger/g1g2.intercept/mc-z.negative.sig.ocn.mgh --csdpdf brianweisinger/g1g2.intercept/mc-z.negative.pdf.dat Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. INFO: loading mask volume: brianweisinger/mask.mgh INFO: MRIbinarize01(): nhits = 118078 Found 118078 voxels in mask Search Space = 118078 mm3 Computing voxel-wise significance CSDpvalMaxSigMap(): found 0/118078 above 0 ERROR: initializing hit map It made some of the CSD files but not all of them. Any ideas? Thank you for your help.

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Freesurfer