Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

mri_binarize to mask and include only positively activated voxels
by Maya Rosen 17 Oct '13

17 Oct '13

Hi Doug/freesurfers, I am now trying to make a mask that includes only positively activated voxels for one conditon versus passive viewing (ConditionAvspassive). Using the inputs that you suggested, I ran the following command: mri_binarize --i ./output_23subjects/fsavg_lh_sm3_nopace_exoltm/ConditionAvpassive/ces.nii.gz --o ./output_23subjects/fsavg_lh_sm3_nopace_exoltm/ConditionAvpassive_mask.ces.nii.gz --mask-thresh 0.00001 --min 0.00001 So my understanding of what this should be doing is making a mask that only includes positively activated voxels compared to passive viewing. However, if you see the attached images of both the mask that this command creates, and the activation maps of ConditionAvpassive (set at a very low threshold for visualization purposes), you can see that there are several regions that are included in the mask that are in fact deactivated compared to passive viewing. Is there something wrong with the command that I'm running that is causing this to happen? Thank you for any insight! Maya

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Extract Cortical Thickness from my data based on ROIs from Qdec
by amirhossein manzouri 17 Oct '13

17 Oct '13

DEar FS experts, I need to extract the CTh from my whole data (90 subjects) based on generated ROI from Qdec(mc-z.neg.th13.sig.ocn.mgh). Would you please advise if I can do it in the same way you have mentioned in this post : http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22973.html -- Best regards, Amirhossein Manzouri

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Freeview Volume & Surface alignment
by Kambiz Tavabi 17 Oct '13

17 Oct '13

I would like to inspect the results of my surface boundary on the volume as per the approach in tkmedit. However in freeview the surface boundary and volume are not aligned in a common space. Why is that? How does one go about aligning the tkregRAS with the RAS? (those are apparently the two different coordinate systems according to the information panel). Thanks in advance. [image: Inline image 1] ------------------------------------------------------------ Kambiz Tavabi PhD Institute for Learning & Brain Sciences 1715 Columbia Road N Portage Bay Building Box 357988 University of Washington Seattle, WA 98195-7988 Tel: 206-685-6173 ------------------------------------------------------------

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tkmedit error message
by Elissa McIntosh 17 Oct '13

17 Oct '13

Hello, I am a new freesurfer user. I tried to view subject data with tkmedit for the first time after the recon-all process finished without errors. Here is what I typed and the message I got: [ariana:~/Desktop/ELISSA_ THESIS/ATO] cmurphy% tkmedit ATO brainmask.mgz -aux T1.mgz -surfs -aseg Wed Oct 16 14:35:57 ariana.local tkmedit.bin[66069] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. xp_init: error: not initialized error: invalid CoreGraphics connection Abort Can someone explain this error message? Despite that the recon-all log said that the subject was completed without error, there were several places in the log that read invalid. Is this normal? Also, I realized that I have an older version of freesurfer and should upgrade. Should I delete the former version and re-install with new version? Thank you for your help, E

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DOSS FS 5.3
by amirhossein manzouri 17 Oct '13

17 Oct '13

Dear Experts, Hi, I have already done my data analysis having group as fixed factor and age as nuisance factor in QDEC FS 5.3. I also need to run it with DOSS. Would you please advise how to run the same analysis with DOSS from terminal and if it is possible to look at the results in QDEC Display again. -- Best regards, Amirhossein Manzouri

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Postdoc position available - Alzheimer's Disease
by Juan Domingo Gispert López 17 Oct '13

17 Oct '13

Postdoctoral Position in Neuroimaging - Pasqual Maragall Foundation, Barcelonabeta Brain Research Center, Barcelona, Spain. Job Summary: Pasqual Maragall Foundation invites applications for a full-time postdoctoral position to conduct post-processing and analyzing of MRI neuroimaging data (e.g. structural, fMRI, DWI), as part of a clinical research program on Alzheimer's disease. Principal Responsibilities: The primary responsibility of this position includes post-processing and analyzing brain MRI data within the Foundation's Alzheimer's disease clinical research and its flagship project, the Alzheimer and Families (ALFA). The ALFA study is a large longitudinal cohort of sons and daughters of Alzheimer's disease (AD) patients, to explore the preclinical stage of this condition with the aim of identifying novel risk factors and biomarkers. This study will enhance our knowledge of the processes involved before the onset of AD to develop interventions aimed to prevent or delay the disease. Within this study we are collecting a comprehensive amount of data, including blood samples, mental health, quality of life and risk factors, as well as, neuroimaging procedures to assess brain function. The Barcelonabeta Brain Research Center (Barcelonabeta) is a new research infrastructure, constituted by the Pasqual Maragall Foundation and with the participation of the Pompeu Fabra University, dedicated to research on Alzheimer's disease. The new building will be completed by summer 2014, and will contain excellent technical facilities including a research-dedicated 3T MR scanner, dedicated to clinical research on neurodegenerative diseases. Barcelonabeta is a research institute affiliated to Pompeu Fabra University and is also part of the Barcelona Biomedical Research Park (PRBB), a large research facility that hosts seven different research institutions related to biomedical research, including the Hospital del Mar Research Institute (IMIM), the Experimental and Health Sciences Department (CEXS) of the UPF, the Regenerative Medicine Centre of Barcelona (CMRB), and the Centre for Research in Environmental Epidemiology (CREAL), among others, in a multidisciplinary, collaborative and stimulating international environment in close contact with a clinical setting, thus conducive to translational research. Required Qualifications: · PhD in Biomedical Engineering, Medical Physics, Neuroscience or related disciplines. · Strong background in MRI analysis and related statistical methods for research (SPM, Freesurfer, FSL or similar). · Experience with image processing and data analysis. · Ability to think independently and work collaboratively. Benefits · Starting date: April 2014. · The postdoctoral position is scheduled initially for three years (open to renewal). · Salary will depend on experience. Additional Information: To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV with list of publications; 3) The names of three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: rh(a)fpmaragall.org Juan D. Gispert Head Neuroimaging Research Pasqual Maragall Foundation T. +34 93 316 09 90 Dr. Aiguader, 88 (Edifici PRBB) - 08003 Barcelona. Spain. http://www.fpmaragall.org/en_index.html ________________________________ Aquest missatge i els seus annexos poden contenir informació confidencial i exclusiva per al destinatari. El seu contingut no constitueix un compromís per part de l'emissor. Si rep aquest missatge per error, si us plau elimini'l sense revisar-lo ni reenviar-lo i notifiqui-ho al remitent. Gràcies per la seva col·laboració. Este mensaje y sus anexos pueden contener información confidencial y exclusiva para el destinatario. Su contenido no constituye un compromiso por parte del emisor. Si recibe este mensaje por error, por favor elimínelo sin revisarlo ni reenviarlo y notifíquelo al remitente. Gracias por su colaboración. This message and attachments may contain confidential and exclusive information intended only for the individual named. The content of this message does not imply any commitment by the sender. If you have received this e-mail by mistake, please delete it before reading or distributing and notify the sender. Thank you for your cooperation. [cid:image006.jpg@01CD0B4C.79CA6620] Gràcies per estalviar paper. Gracias por ahorrar papel.Thanks for saving paper.

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-hippo-subfields error
by Garikoitz Lerma-Usabiaga 17 Oct '13

17 Oct '13

Hi, I had a subject already run through recon-all. After making recon-all -s ID -hippo-subfields or recon-all -s ID -hippo-subfields -make all it is failing. It is the first subject ever failing with the hippo-subfields. The rest of the subjects are ok. This subject is properly segmented (tkmedit ID brainmask.mgz -surfs -aseg is ok). Any recommendations on what to do next? thanks! Gari PS1 please find attached the last recon-all invocation log. PS2 I have the screen output as well, there was more detail in that, in case it would help recognizing the problem.

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Re: [Freesurfer] Easiest way to resample a volume..?
by Rudolph Pienaar 16 Oct '13

16 Oct '13

Thanks, Jon -- although the '-ds' seems depreciated: [paris:x86_64-Linux-chb-fs-stable]...olphpienaar/tmp$>mri_convert -vs 1 1 1 -ds 0.25 0.25 0.25 BM05_recon.nii BM05_recon3.nii mri_convert -vs 1 1 1 -ds 0.25 0.25 0.25 BM05_recon.nii BM05_recon3.nii mri_convert: unknown flag "-ds" type mri_convert -u for usage On 10/16/13 16:07 , Jon Wieser wrote: > mri_convert can change the voxel resolution for you > > > mri_convert -vs 1 1 1 -ds 0.33 0.33 0.33 <filename> > > > see the help: > https://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html > > Jon > > ----- Original Message ----- > From: "Rudolph Pienaar" <rudolph(a)nmr.mgh.harvard.edu> > To: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, October 16, 2013 2:36:37 PM > Subject: [Freesurfer] Easiest way to resample a volume..? > > Hi all -- > > I have a volume of say 100x100x100 1mm^3 and I'd like to resample it to > 300x300x300 0.33mm^3. > > What's the easiest way to do this? Will 'mri_convert' do the trick? > > Best > -=R > -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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Re: [Freesurfer] Easiest way to resample a volume..?
by Rudolph Pienaar 16 Oct '13

16 Oct '13

Perfect! That worked :-) Thanks On 10/16/13 16:03 , Juan Eugenio Iglesias wrote: > Hi Rudolph, > yes, you can use mri_convert with the flag -vs 0.333333 0.333333 0.333333 > You might want to play with -rt as well to switch from linear to cubic > resampling. > Cheers, > /Eugenio > > > On 10/16/2013 03:36 PM, Rudolph Pienaar wrote: >> Hi all -- >> >> I have a volume of say 100x100x100 1mm^3 and I'd like to resample it to >> 300x300x300 0.33mm^3. >> >> What's the easiest way to do this? Will 'mri_convert' do the trick? >> >> Best >> -=R >> > -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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Easiest way to resample a volume..?
by Rudolph Pienaar 16 Oct '13

16 Oct '13

Hi all -- I have a volume of say 100x100x100 1mm^3 and I'd like to resample it to 300x300x300 0.33mm^3. What's the easiest way to do this? Will 'mri_convert' do the trick? Best -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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Freesurfer October 2013