Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

FSL registration
by Jones, Richard 29 Apr '14

29 Apr '14

I have T1 data that has been run through freesurfer and I want to apply the subcortical parcellations from that analysis to some QSM data. The mailing list and website refer to using reg-feat2anat but this require an existing feat directory. If I make a "pseudo" feat directory with my QSM data so that I can use reg-feat2anat does it just need to contain the subfolder reg containing the the QSM data as "example_func.nii" and the registration matrix from using FLIRT to register the QSM data to MNI space as "example_func2standard.mat", or is there something else that needs to be included? Thanks, Richard

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incongruent coordinates in freeview and *sig.cluster.summary
by charujing123 29 Apr '14

29 Apr '14

Hi all, I have done group analysis and see it in freeview. Also I can see my sig.cluster.summary file to find clusters those survived. As I know, the MNIX MNIY MNIZ in the cluster summary file is coordinates for the maximum. The coordinate system is MNI305. Also I input the vertex number at the maximum in freeview, but it echo different coordinate for the vertex from that in cluster summary file. Why? Another question. There is "RAS" symbol at the bottom of freeview window. However I see the coordinates : inferior, posterior, left is negtive, superior, anterior,and right is positive. I suspect the coordinate system is LPI. Is that right? Thanks. All the best. Rujing Zha 2014-04-26 charujing123

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R: Re: thalami mask (nii.gz) to import in FSL
by stdp82＠virgilio.it 29 Apr '14

29 Apr '14

My apologies, how can I visualize mri_binarize output? I tried in fslview but orientation is wrong. Different orientation is a file's feature or swapdim is request? Thanks, Stefano ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 29-apr-2014 16.01 A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL Hi Stefano you can use either mri_binarize --match or mri_extract_label with labels 10 and 49 (which I got from FreeSurferColorLUT.txt) cheers Bruce On Tue, 29 Apr 2014, stdp82(a)virgilio.it wrote: > Hi list, > I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it as seed > mask in probtrackx. > > Thanks, > > > Stefano > >_______________________________________________ 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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Two Research Assistant Positions at Boston Children's Hospital
by Gaab, Nadine 29 Apr '14

29 Apr '14

Research Assistant Positions at Boston Children's Hospital: Pediatric and Infant (f)MRI/developmental cognitive neuroscience/typical and atypical reading development GaabLab at Children's Hospital Boston Developmental Medicine Children's Hospital Boston RESEARCH STUDY ASSISTANTS: Children's Hospital Boston (Harvard Medical School); Developmental Medicine Center, Laboratories of Cognitive Neuroscience: A) Technical Research Study Assistant to join the Gaab Lab www.childrenshospital.org/research-and-innovation/research-labs/gaab-labora…<http://www.childrenshospital.org/research-and-innovation/research-labs/gaab…> and (www.babymri.org<http://www.babymri.org/>) to assist with all study phases of functional and structural MRI for several projects. This includes design and implementation of experiments; help with operation of MRI scanner, implementation and maintenance of analysis software; technical support for lab personnel. Advanced computer skills required. This position is ideal for anyone considering future graduate study in cognitive (developmental) neuroscience, computer science, cognitive science or neuroscience. Bachelor's Degree in computer science, psychology, cognitive science, neuroscience, math, or related field required. Comfort with a heterogeneous computing environment (Linux/Unix, Mac, and Windows) as well as some programming experience required; knowledge of psychological experiment software (E Prime, Presentation, etc.) and/or fMRI analyses software helpful. Demonstrable pre-existing interest in cognitive neuroscience desired; knowledge of neuroanatomy or statistics helpful. Must be self-motivated and able to work in a fast-paced, changing environment and must like working with children. Start date June/July 2014 or later; 18 months commitment preferred. Please send application package to Nadine Gaab Nadine.gaab(a)childrens.harvard.edu<mailto:Nadine.gaab@childrens.harvard.edu> B) Research Study Assistant to join the Gaab Lab www.childrenshospital.org/research-and-innovation/research-labs/gaab-labora…<http://www.childrenshospital.org/research-and-innovation/research-labs/gaab…> and (www.babymri.org<http://www.babymri.org/>) to assist with day-to day operations and functions and development and implementation of research procedures. This includes subject recruitment for pediatric research studies which will include close interaction with schools in the Boston area, scheduling of pediatric research subjects, database maintenance, pediatric testing (including MRI/fMRI scanning of young children and infants [see www.babymri.org<http://www.babymri.org>]) and data analyses (psychometrics, psychophysics and functional magnetic imaging), stimuli design and administrative work (e.g.; preparation of internal review board proposals). Demonstrable pre-existing interest in cognitive neuroscience desired; knowledge of project management, psychological experiment software (e.g.: Eprime or Presentation) or statistics helpful. Advanced computer skills highly desirable but not required. Bachelor's Degree in psychology, education, child development, cognitive science, neuroscience, or related field required. Must be self-motivated and able to work in a fast-paced, changing environment and must like working with children and families. Start date June/July 2014 or later; 18 months commitment preferred. Please send application package to Nadine Gaab Nadine.gaab(a)childrens.harvard.edu<mailto:Nadine.gaab@childrens.harvard.edu> "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955) Nadine Gaab, PhD Assistant Professor of Pediatrics Boston Children's Hospital/Harvard Medical School Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience 1 Autumn Street (Office 643); Boston, MA 02115 nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu> phone: 857-218-3021 www.childrenshospital.org/research-and-innovation/research-labs/gaab-labora…<http://www.childrenshospital.org/research-and-innovation/research-labs/gaab…> www.babymri.org

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Re: [Freesurfer] A newbie to fMRI analysis
by Shantanu Ghosh 29 Apr '14

29 Apr '14

Hi Sampada, Please cc the freesurfer list when answering/asking questions so others can answer too. And also people with similar issues will benefit from the discussion. see inline for my responses. Hth, shantanu On Mon, April 28, 2014 8:27 pm, Dr Sampada Sinha wrote: > Hello Shantanu, > > Thanks for your reply.I tried using that as well. And it says that the > file > is only 'read' file. I used chmod on unix but still its not working with > dcm2nii. Interstingly, when I used mriconvert software for this,it > converted all the dcm files to .img/.hdr files. This process resulted in > eight folders (in .img/.hdr format) in the order of > T1>T2>T1>T2>DTI>T1(resting stage)>T2 (in the order of the acquisition > acquired at the time of experiment). > Is there any special command you are using to convert those files > Shantanu? You can edit dcm2nii.ini file using any text editor after it is created automatically (by running dcm2nii for the first time). It operates like a shell program and can be run from your analysis directory by sourcing it first. If you look at the dcm2nii file you can use custom settings. To get the output nii as a single file set the SingleNIIFile=1 and 4D=1, otherwise by default you get the img/hdr pairs If further you want nii.gz instead of nii files, use Gzip=1 setting If this doesn't work, you could use the Windows version to convert with the same settings that I describe above. > If yes, will you please let me know? Where do you keep your dcm files > (iyou > don't mind me asking that)? I tried changing the location from Desktop to > Applications/freesurfer as well, but its still not working. The dcm files can be anywhere, you have to source them correctly by providing the correct path. Or drag/drop into the window if you are using the gui. > > Thanks and regards, > > Sampada > > > > On Mon, Apr 28, 2014 at 7:00 PM, Shantanu Ghosh < > shantanu(a)nmr.mgh.harvard.edu> wrote: > >> You can convert Dicom using MRICroN with the dcm2nii utility >> >> shantanu >> >> >> On Mon, April 28, 2014 6:55 pm, Dr Sampada Sinha wrote: >> > Hello I have only recently started the fmri data analysis and I >> downloaded >> > freesurfer point by point from martinos site and incorporated the >> license >> > file as well into the Applications/freesurfer directory. I have run >> into >> > the first problem and that is of data conversion. My file is in dcm >> format >> > and I have 11,000 dcm files to convert. However, before I was using >> Jamaan >> > Alghamadi created gui and it is not able to convert the mri dcm files. >> > Then I shifted to UNIX and again it is saying error. >> > >> > My file is on the desktop and I have given it subject id as Grace. My >> > directory to the dcm file is '/Users/sampada/desktop/Grace. >> > >> > My terminal look like this before I proceed with the file conversion >> > >> > Last login: Mon Apr 28 15:10:13 on ttys001 >> > >> > dhcp020-223-179:~ sampada$ export >> FREESURFER_HOME=/Applications/freesurfer >> > >> > dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh >> > >> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- >> > >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> > >> > FREESURFER_HOME /Applications/freesurfer >> > >> > FSFAST_HOME /Applications/freesurfer/fsfast >> > >> > FSF_OUTPUT_FORMAT nii.gz >> > >> > SUBJECTS_DIR /Applications/freesurfer/subjects >> > >> > MNI_DIR /Applications/freesurfer/mni >> > >> > >> > >> > Will anyone please let me know what I am doing wrong? I will be very >> > grateful for any input. >> > >> > >> > Thanks and regards, >> > >> > >> > Sampada >> > Senior research support specialist >> > Molecular and neuroimaging department >> > Department of Psychiatry >> > 451, biomedical research building >> > University at Buffalo (south campus) >> > Buffalo, NY-14216 >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Shantanu Ghosh, Ph.D. >> Harvard Medical School & Massachusetts General Hospital >> Martinos Center for Biomedical Imaging >> -- >> Not only is the universe stranger than we think, it is stranger than we >> can think. -Werner Heisenberg >> >> _______________________________________________ >> 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. >> >> > -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg

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R: Re: thalami mask (nii.gz) to import in FSL
by stdp82＠virgilio.it 29 Apr '14

29 Apr '14

My apologies, how can I visualize mri_binarize output. I tried in fslview but orientation is wrong. Different orientation is a file's feature or swapdim is request? Thanks, Stefano ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 29-apr-2014 16.01 A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL Hi Stefano you can use either mri_binarize --match or mri_extract_label with labels 10 and 49 (which I got from FreeSurferColorLUT.txt) cheers Bruce On Tue, 29 Apr 2014, stdp82(a)virgilio.it wrote: > Hi list, > I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it as seed > mask in probtrackx. > > Thanks, > > > Stefano > >_______________________________________________ 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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thalami mask (nii.gz) to import in FSL
by stdp82＠virgilio.it 29 Apr '14

29 Apr '14

Hi list, I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it as seed mask in probtrackx. Thanks, Stefano

2 1

Re: [Freesurfer] A newbie to fMRI analysis
by Dr Sampada Sinha 28 Apr '14

28 Apr '14

Hello Shantanu, Thanks for your reply.I tried using that as well. And it says that the file is only 'read' file. I used chmod on unix but still its not working with dcm2nii. Interstingly, when I used mriconvert software for this,it converted all the dcm files to .img/.hdr files. This process resulted in eight folders (in .img/.hdr format) in the order of T1>T2>T1>T2>DTI>T1(resting stage)>T2 (in the order of the acquisition acquired at the time of experiment). Is there any special command you are using to convert those files Shantanu? If yes, will you please let me know? Where do you keep your dcm files (iyou don't mind me asking that)? I tried changing the location from Desktop to Applications/freesurfer as well, but its still not working. Thanks and regards, Sampada On Mon, Apr 28, 2014 at 8:27 PM, Dr Sampada Sinha <drsampadasinha(a)gmail.com>wrote: > Hello Shantanu, > > Thanks for your reply.I tried using that as well. And it says that the > file is only 'read' file. I used chmod on unix but still its not working > with dcm2nii. Interstingly, when I used mriconvert software for this,it > converted all the dcm files to .img/.hdr files. This process resulted in > eight folders (in .img/.hdr format) in the order of > T1>T2>T1>T2>DTI>T1(resting stage)>T2 (in the order of the acquisition > acquired at the time of experiment). > Is there any special command you are using to convert those files > Shantanu? If yes, will you please let me know? Where do you keep your dcm > files (iyou don't mind me asking that)? I tried changing the location from > Desktop to Applications/freesurfer as well, but its still not working. > > Thanks and regards, > > Sampada > > > > On Mon, Apr 28, 2014 at 7:00 PM, Shantanu Ghosh < > shantanu(a)nmr.mgh.harvard.edu> wrote: > >> You can convert Dicom using MRICroN with the dcm2nii utility >> >> shantanu >> >> >> On Mon, April 28, 2014 6:55 pm, Dr Sampada Sinha wrote: >> > Hello I have only recently started the fmri data analysis and I >> downloaded >> > freesurfer point by point from martinos site and incorporated the >> license >> > file as well into the Applications/freesurfer directory. I have run into >> > the first problem and that is of data conversion. My file is in dcm >> format >> > and I have 11,000 dcm files to convert. However, before I was using >> Jamaan >> > Alghamadi created gui and it is not able to convert the mri dcm files. >> > Then I shifted to UNIX and again it is saying error. >> > >> > My file is on the desktop and I have given it subject id as Grace. My >> > directory to the dcm file is '/Users/sampada/desktop/Grace. >> > >> > My terminal look like this before I proceed with the file conversion >> > >> > Last login: Mon Apr 28 15:10:13 on ttys001 >> > >> > dhcp020-223-179:~ sampada$ export >> FREESURFER_HOME=/Applications/freesurfer >> > >> > dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh >> > >> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- >> > >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> > >> > FREESURFER_HOME /Applications/freesurfer >> > >> > FSFAST_HOME /Applications/freesurfer/fsfast >> > >> > FSF_OUTPUT_FORMAT nii.gz >> > >> > SUBJECTS_DIR /Applications/freesurfer/subjects >> > >> > MNI_DIR /Applications/freesurfer/mni >> > >> > >> > >> > Will anyone please let me know what I am doing wrong? I will be very >> > grateful for any input. >> > >> > >> > Thanks and regards, >> > >> > >> > Sampada >> > Senior research support specialist >> > Molecular and neuroimaging department >> > Department of Psychiatry >> > 451, biomedical research building >> > University at Buffalo (south campus) >> > Buffalo, NY-14216 >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Shantanu Ghosh, Ph.D. >> Harvard Medical School & Massachusetts General Hospital >> Martinos Center for Biomedical Imaging >> -- >> Not only is the universe stranger than we think, it is stranger than we >> can think. -Werner Heisenberg >> >> _______________________________________________ >> 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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order of edits and autorecon commands
by Elissa McIntosh 28 Apr '14

28 Apr '14

This is a basic question about the process for manual edits and the autorecon commands. I am going to follow the recommended reconstruction page (on fs wiki) to make manual edits on my data. The page says that you can make all the manual edits at once. But my question is, how do you go about running the autorecon commands specific to each type of edit? Do you run each command separately after you're done saving all your manual edits? It seems that some of the steps are redundant (like running autorecon 3 more than once). Also, if I make changes to skullstip, will I have to do the recon again before doing additional edits? Here is an example where my questions would need to be addressed. Say I had to add control points to wm, and erase some voxels from the pial. Do I make edits and run the commands to fix these problems separately (i.e. make wm edits and subsequently run appropriate recon steps specified in wiki, then make pial edits and run specified recon steps), or do I make any types of edits at once (control points, add/delete voxels, etc.) and then run each command separately, or do I make any types of edits at once and somehow combine these different commands into one step? I'm sorry if this is confusing - I am just trying to grasp how to approach manual edits in the "order" listed in the recommended reconstruction page. Thank you! Elissa

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Extract ROI from anatomical volume
by pfotiad＠nmr.mgh.harvard.edu 28 Apr '14

28 Apr '14

Hi FS experts, I was wondering what the best way to extract an ROI from an anatomical volume would be. For instance, I would like to create a volume of only the wm-lh-precentral based on the orig.mgz volume and on the segmentation map wmparc.mgz. I know that something similar can be done with the mri_extract_label command, but if I'm not mistaken that command can only be applied to a segmentation volume, and not on an anatomical volume like orig.mgz. Thanks in advance, Panos

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Freesurfer