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30090 discussions

correlation between resting state fmri and brain perfusion
by Chen, Yasheng 03 Jun '13

03 Jun '13

Hi all, Sorry to post a question not related to the brain surface analysis. I wonder why there are not many studies looking into the correlation between perfusion and resting state fmri. Perfusion should play an important role in modulating resting bold signal. Does any one have some experience using either ASL or perfusion measurement from PET to look into how these things are correlated? Is this an area worth pursuing? Thank you very much! Yasheng

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Fwd: Fwd: mir_convert produces a darkened file
by Erin Browning 03 Jun '13

03 Jun '13

It seems like it getting darker messes up the normalization later on; could this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and here's what it looks like after we run motioncor (1029-orig.jpg). On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > that will not change the intensities at all. It is probably just a display > issue. Try changing the brightness/contrast. The artifact might cause > problems later on, but this is not an issue I think > doug > > > On 06/03/2013 02:20 PM, Erin Browning wrote: > >> We use: >> >> mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz >> >> where freesurfer is our freesurfer subject folder. >> >> >> On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >> wrote: >> >> what is your mri_convert command line? >> >> On 06/03/2013 02:11 PM, Erin Browning wrote: >> > Hi everyone-- >> > >> > We have a series of scans with an hyperintense artifact cutting >> > through the temporal and frontal lobe. When we run mri_convert to >> > convert from AFNI .BRIK files to .mgz fles, the results look >> like the >> > attached image. >> > >> > How can I correct for this? We tried skullstripping in AFNI first to >> > remove some of the artifact, but that didn't seem to help very much. >> > >> > Thank you, >> > Erin Browning >> > >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >

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Group Analysis Question
by Fotiadis, Panagiotis 03 Jun '13

03 Jun '13

Hey Doug, I have run a group analysis on my data with two different ways. (The input is cortical thickness.) In the first analysis, I specified 4 groups (Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas in the second, just two groups (Diseased, Healthy). One of the comparisons that I did was the age slope between Diseased and Healthy. Therefore in the first analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 -0.5] and in the second analysis I set it to [0 0 1 -1]. However, the results that came up were somewhat different. For instance there were clusters in the second analysis that were significant but were not significant in the first analysis. Shouldn't the results be the same? Thank you, Panos

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Fwd: mir_convert produces a darkened file
by Erin Browning 03 Jun '13

03 Jun '13

Hi everyone-- We have a series of scans with an hyperintense artifact cutting through the temporal and frontal lobe. When we run mri_convert to convert from AFNI .BRIK files to .mgz fles, the results look like the attached image. How can I correct for this? We tried skullstripping in AFNI first to remove some of the artifact, but that didn't seem to help very much. Thank you, Erin Browning

2 3

Fwd: autorecon3 error
by Claudia Dacquino 03 Jun '13

03 Jun '13

Hi Freesurfers, I did autorecon3-cp and exited with errors. Ould anyone help me to understand what's the roblem? You can find the recon-all.log attached. Thanks in advance. Claudia

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Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.
by Douglas N Greve 03 Jun '13

03 Jun '13

Hi Rito, I don't think we report a total wm volume, do we? doug On 06/03/2013 12:56 PM, Ritobrato Datta wrote: > Hi Doug, > > Just following up on your reply sometime back - > Does total white volume include cerebellar wm vol also ? > > Please let me know. > > Thanks > > Rito > > ----- Original Message ----- > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > To: freesurfer(a)nmr.mgh.harvard.edu > Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT) > Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol. > > Total Gray includes the cerebellar gray > doug > On 05/24/2013 03:51 PM, Ritobrato Datta wrote: >> Hello All, >> >> Can someone address the following ? I sent this query yesterday but it fell through the cracks. >> >> I am using freesurfer 5.1 for my analysis. >> >> I am interested in calculating the whole brain vol (total Gray vol + total WM vol) excluding the CSF volume and cerebellum. >> >> Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol >> >> In all of the 79 subjects, when I compare the Total Brain Vol to SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain Vol I have calculated. >> >> Here are some measures - >> >> For 79 subjects - >> >> Average Total Brain Vol = 1038395.291 >> >> Average SupraTentorialVol = 979996.4684 >> >> Is that expected ? >> >> Is it possible that CSF vol is part of Total Brain Vol ? >> >> Any insight will be helpful. >> >> Thanks >> >> Rito >> >> _______________________________________________ >> 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. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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combination of different surfaces across the group for mri_glmfit statistics
by Robert Schulz 03 Jun '13

03 Jun '13

Hi, I have two questions: 1. I have created specific surfaces in fsaverage rh for each of my 20 subjects. (xy.mgh) I'd like to run statistical analysis within the common surface area which is included in all subjects. Therefore I wonder how to combine those surfaces. My idea would be to add all surfaces and threshold the resulting surface by 20 ==> giving a final surface common to all of them. 2. How can I limit mri_glmfit to this final surface to run the statistical analysis only in this area, not in all of the hemisphere? Can anybody provide the appropriate commands for both issues? Thank you very much! Best wishes, Robert -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Astrid Lurati (Kommissarisch), Joachim Prölß, Matthias Waldmann (Kommissarisch) Bitte erwägen Sie, ob diese Mail ausgedruckt werden muss - der Umwelt zuliebe. Please consider whether this mail must be printed - please think of the environment.

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Bug report: fslregister within reg-feat2anat
by Chris Adamson 03 Jun '13

03 Jun '13

During the reg-feat2anat script fslregister produces errors. I tracked it to the argument parsing code 419 case "--fsvol": 420 if ( $#argv < 1) goto arg1err; 421 set fsvol = $argv[1]; shift; 422 set tmp = `fname2stem $fsvol`; 423 if(! $status) set fsvol = $tmp; 424 breaksw The reg-feat2anat script uses the following call: ./fslregister --s *** --reg ***+.feat/reg/freesurfer/anat2exf.register.dat --mov ***+.feat/example_func.nii --dof 6 --bins 256 --cost corratio --fslmat ***+.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat ***+.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp ***+.feat/reg/freesurfer/tmp --out ***+.feat/reg/freesurfer/tmp/exf-in-anat.nii and the fsvol variable is eventually set ERROR: because line 422 fails. fsvol originally is just "brainmask" but it requires the full filename for fname2stem to work. Also, if I change the line 422 to $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz the rest of the script fails because it expects to just have "brainmask" not the full path. FS VOL FIRST brainmask Before stem brainmask /data/***********/mri/brainmask TMP ERROR: cannot determine stem FS VOL FIRST AFTER RETURN ERROR: -- Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash) Research Officer Developmental Imaging, Critical Care and Neurosciences Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road, Parkville,Victoria, 3052, Australia T 9906 6780 M XXXX XXX XXX E chris.adamson(a)mcri.edu.au www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

3 2

Defacing with mri_deface
by slehar＠nmr.mgh.harvard.edu 03 Jun '13

03 Jun '13

The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files /usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca The former exists where it should, the latter does not exist at that location, although it can be downloaded from http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads and gunzipped. When I copy it into a directory and call mri_deface directly, it works OK because it can find that image locally. But when I call recon-all with the -deface flag, it looks for the file where it does not exist, i.e. /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca Could someone with the appropriate permissions please copy that file to where recon-all expects to find it? Second question: If I call recon-all with the -deface flag, does it deface ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only deface a copy of orig.mgz to orig_defaced.mgz?

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use of anot_2_label
by LAOUCHEDI MAKHLOUF 03 Jun '13

03 Jun '13

Hi i used mri_annotation2label to extract the cortical labels. for this command we must specify which hemisphere (--hemi ?h) and i want to extract the brainstem which is not a lateralized structure, is there any command like mri_annotation2label to extract the brainstem ? thanks

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