Freesurfer

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30088 discussions

rtview: trouble finding files
by Michelle Umali 13 Oct '11

13 Oct '11

Dear Freesurfers, I know this is a very simple question. I'm just having trouble specifying the correct directories for rtview based on the example. When I run rtview, it can't find the image files that really do exist in the directory. For the following example in the help section: I did what I thought were the proper replacements Example: cd sess/bold/rtopy.lh rtview --s subject --lh --eccen \ --real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii What I did: cd $SUBJECTS_DIR/retinotopy/sj07/bold/rtopy.self.lh rtview --s sj07 --lh --eccen \ --real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii Then I tried getting rid of the --s and --lh flags because I was already in that directory, but that didn't help either. If I'm already in the in the correct folder why do I still have to specify --s and --lh? Thanks. Michelle

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Group Average of Retinotopy Results
by Michelle Umali 12 Oct '11

12 Oct '11

Hi Doug, I'm a little confused as to how to assign functional data to the fsaverage space. 1) Do you mean just change each subject's subjectname file to fsaverage and then do the same thing as before for each person? 2) Also, when I specify the analysis do I change -rtopy.self.lh to rtopy.fsaverage.lh, i.e. will isconcat later be sensitive to analysis name? e.g. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force then the same for selxavg3-sess and fieldsign-sess and then isxconcat-sess would be: isxconcat-sess -sf sessid -analysis rtopy.fsaverage.lh -o group_lh Thanks. Michelle

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QDEC labels vs annotations
by krista kelly 12 Oct '11

12 Oct '11

I'm using the labels saved in QDEC to extract cortical thickness values for certain regions. For example, I've used the lh.v1.label to map onto the fsaverage brain and then to map this onto each individual subject. When I load the lh.PALS_B12_Brodmann.annot or the lh.PALS_B12_Visuotopic.annot onto the fasaverage brain, the areas that are named v1 do not quite match up with the actual lh.v1.label. The more inferior part of the lh.v1.label is considered v2 in the the annotation space. Should I be worried about this? Or can I still use the lh.v1.label to extract information for v1 (even though the annotation file would consider it v2). Thanks!

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Group Average of Retinotopy Results
by Michelle Umali 12 Oct '11

12 Oct '11

Dear Freesurfers, I've generated individual polar, eccentricity, and fieldsign maps for each of my subjects. I would like to generate group average maps of these that I can visualize on the fsaverage brain. When I ran: isxconcat-sess -sf sessid -analysis rtopy.self.lh -o group_lh I got: ERROR: analysis space is self surface, not supported How do I do a group average for the 3 different maps? Thanks. Michelle For each person I ran recon-all and flattened occipital patches. Then: mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sjXX -fsd bold -force selxavg3-sess -a rtopy.self.lh -s sjXX -force selxavg3-sess -a rtopy.self.rh -s sjXX -force fieldsign-sess -a rtopy.self.lh -occip -fwhm 20 -s sjXX fieldsign-sess -a rtopy.self.rh -occip -fwhm 20 -s sjXX

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Brain stem volume
by Lugar, Heather 12 Oct '11

12 Oct '11

I was wondering if Freesurfer has a standard way of cutting off the measurement of brain stem volume across subjects, or does the volume of the brain stem depend on the individual's skull strip? In the two examples below, you can see that the brain stem of the second individual extends beyond that of the first (visually and according to its aseg label). Theoretically, could the reported volumes of these two individuals' brain stems be different just because their skull strip was different? Thank you, Heather [cid:image001.png@01CC88D6.715115A0] [cid:image002.png@01CC88D6.715115A0]

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Re: [Freesurfer] WM hypointensities and corpus callosum mislabeling
by Warren Winter 12 Oct '11

12 Oct '11

Let me try this again. Here's one that mislabeled parts of the CC as left cerebral white matter at the center slice: Another one mislabels nearly the entire CC at the center slice: Here you can see the light purple blotches above the caudate (light blue); those are labeled as white matter hypointensities: And again here: The overall quality is not great, but we're trying to make the best of what we have. Any advice on correcting these common problems in our dataset (apart from manually doctoring them) would be greatly appreciated! Warren On Oct 11, 2011, at 6:44 PM, Warren Winter wrote: > Here's one that mislabeled parts of the CC as left cerebral white matter at the center slice: > > <Screen shot 2011-10-11 at 6.31.19 PM.png> > Another one mislabels nearly the entire CC at the center slice: > > <Screen shot 2011-10-11 at 6.21.35 PM.png> > > You can see the light purple blotches above the caudate (light blue); those are labeled as white matter hypointensities. > > <Screen shot 2011-10-11 at 6.31.05 PM.png> > > And again here: > > <Screen shot 2011-10-11 at 6.20.18 PM.png> > > The overall quality is not great, but we're trying to make the best of what we have. Any advice on correcting these common problems in our dataset (apart from manually doctoring them) would be greatly appreciated! > > Warren > > On Oct 10, 2011, at 7:59 PM, Bruce Fischl wrote: > >> Hi Warren >> >> can you send us some images to show us what you mean? Or upload an >> example dataset for us to look at? >> >> cheers >> Bruce >> On Mon, 10 Oct 2011, Warren Winter wrote: >> >>> Hello, >>> In a number of our subjects I've been finding white matter hypointensities around the anterior edge of the caudate, as well as mislabelings of the corpus callosum as cerebral >>> white matter (at and/or around slice 128, sagittal). Has anyone else encountered these problems, and are there fixes that don't involve manually doctoring the mislabelings >>> (such as setting a particular flag for recon)? >>> >>> I am quite new to FS so please forgive any rudimentary misunderstandings. >>> >>> Thank you! >>> >>> Warren >>> >>> -- >>> Warren Winter >>> Lab Coordinator >>> Children's Hospital Boston >>> Division of Developmental Medicine >>> 1 Autumn Street, AU 650 >>> Boston, MA 02215 >>> 857-218-5224 >>> >>> >>> >> >> >> 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. > > -- Warren Winter Research Coordinator Children's Hospital Boston Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224

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graph of region neighborhood
by Satrajit Ghosh 12 Oct '11

12 Oct '11

hi folks, do you happen to have any tool/script that produces a graph of aparc region neighborhood? with perhaps the edge weight being the length of shared boundary. cheers, satra

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.img unsupported data type ?
by m.vlutters 11 Oct '11

11 Oct '11

Dear FreeSurfers, First of all, I am completely new to FS so forgive me if I missed something simple. I am currently running freesurfer v5.1.0, using the .vdi file with VirtualBox. (Host = windows 7). I tested the program by running the autorecon1 on subject "bert" and everything seems to work fine so far. Now I have a .img file (which I can view using SPM8), and I would like to convert it to a .mgz file using freesurfer's mri_convert. I tried the following: mri_convert /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img /home/virtualuser/freesurfer/subjects/MySubj/001 -ot mgz which gives me: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img... ReadAnalyzeHeader: unsupported data type 0 If I specify the input type as well (-it spm) I get: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img... ERROR: CountAnalyzeFiles: file with.img extension specified with zero pad variable. I tried it with other .img files I have as well and I get similar errors. (Sometimes with a different number behind 'unsupported data type', like -12080) What am I doing wrong? Does it have something to do with this zero pad variable? I don't expect the .img files to be wrong. They are generated by SPM8. Thanks in advance for any replies! Mark V

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Re: [Freesurfer] WM hypointensities and corpus callosum mislabeling
by Bruce Fischl 11 Oct '11

11 Oct '11

Hmmm, can you upload a couple of examples? On Oct 11, 2011, at 6:44 PM, Warren Winter <Warren.Winter(a)childrens.harvard.edu> wrote: > Here's one that mislabeled parts of the CC as left cerebral white matter at the center slice: > > <Screen shot 2011-10-11 at 6.31.19 PM.png> > Another one mislabels nearly the entire CC at the center slice: > > <Screen shot 2011-10-11 at 6.21.35 PM.png> > > You can see the light purple blotches above the caudate (light blue); those are labeled as white matter hypointensities. > > <Screen shot 2011-10-11 at 6.31.05 PM.png> > > And again here: > > <Screen shot 2011-10-11 at 6.20.18 PM.png> > > The overall quality is not great, but we're trying to make the best of what we have. Any advice on correcting these common problems in our dataset (apart from manually doctoring them) would be greatly appreciated! > > Warren > > On Oct 10, 2011, at 7:59 PM, Bruce Fischl wrote: > >> Hi Warren >> >> can you send us some images to show us what you mean? Or upload an >> example dataset for us to look at? >> >> cheers >> Bruce >> On Mon, 10 Oct 2011, Warren Winter wrote: >> >>> Hello, >>> In a number of our subjects I've been finding white matter hypointensities around the anterior edge of the caudate, as well as mislabelings of the corpus callosum as cerebral >>> white matter (at and/or around slice 128, sagittal). Has anyone else encountered these problems, and are there fixes that don't involve manually doctoring the mislabelings >>> (such as setting a particular flag for recon)? >>> >>> I am quite new to FS so please forgive any rudimentary misunderstandings. >>> >>> Thank you! >>> >>> Warren >>> >>> -- >>> Warren Winter >>> Lab Coordinator >>> Children's Hospital Boston >>> Division of Developmental Medicine >>> 1 Autumn Street, AU 650 >>> Boston, MA 02215 >>> 857-218-5224 >>> >>> >>> >> >> >> 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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Re: [Freesurfer] Talairach transformation
by Maria Felber 11 Oct '11

11 Oct '11

Dear all, indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria ----- Original Message ----- From: "Avi Snyder" <avi(a)npg.wustl.edu> To: "Sita Kakunoori" <sita(a)nmr.mgh.harvard.edu>, felber(a)cbs.mpg.de, "Avi Snyder" <avi(a)npg.wustl.edu> Cc: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation Hi Sita, Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible. Avi ----------------------------------------------- On 9/13/11 2:26 PM, "Sita Kakunoori" <sita(a)nmr.mgh.harvard.edu> wrote: > >I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this >e-mail. >Hi Dr.Snyder, Not sure if you remember but we saw something similar in a >dataset here at the center where the talairach was much smaller than the >orig.mgz volume and you created a new talairach template to be used with >that dataset. I just wondered if this issue is similar to that. > >Thanks much, >Sita. >---------- Forwarded message ---------- >Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) >From: Maria Felber <felber(a)cbs.mpg.de> >To: freesurfer(a)nmr.mgh.harvard.edu >Subject: [Freesurfer] Talairach transformation > >Hi Bruce, > >so we are back at the beginning. After I ran recon-all -all, I did >exactly that and checked the xform using tkregister2. And here I always >see that my talairach volume (the transform) is always smaller, which can >be very well seen as the orig surfaces of the subjects are always a >little outside the brain and reach well into the skull areas. Of course I >can make the adjustments as descriped in the short instructions. But this >also means I ran the recon-all precess anew for another 30 h per subject. >And that is the reason, why I asked if this is normal that the tailarach >transform is a) always smaller than the original brain, and b) if I can >make any adjustments to prevent that from happening and thus saving >another 30h per subject. >In short: How acurate hat the talairach.xfm has to be and is it possible >to change some parameters to make this transformation a little more >accurate while running the recon-all process only once? >Best, >Maria > > >----- Original Message ----- >From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> >To: "Maria Felber" <felber(a)cbs.mpg.de> >Cc: freesurfer(a)nmr.mgh.harvard.edu >Sent: Tuesday, September 13, 2011 4:07:55 PM >Subject: Re: [Freesurfer] Talairach transformation > >Hi Maria > >you can use tkregister2 to check the accuracy of the talairach.xfm >transform ("xform" for short), and correct it if you want. > >cheers >Bruce >On Tue, 13 Sep 2011, Maria Felber wrote: > >> Hi Bruce, >> >> thanks for the first response. I tried to find some information on the >>webpage about xform, but failed. So what is xform standing for and >>where/how can I check it? >> As in the later processing stages I want to do localization and >DCM-Modeling with my data, I guess the correct talairach coords are kind >of >important for later comparisons. >> Thanks again, >> Maria >> >> ----- Original Message ----- >> From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> >> To: "Maria Felber" <felber(a)cbs.mpg.de> >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Sent: Friday, September 9, 2011 2:13:05 PM >> Subject: Re: [Freesurfer] Talairach transformation >> >> Hi Maria >> >> as long as the tal xform is reasonable I wouldn't worry about it, unless >> for some reason you care a lot about the accuracy of the talairach >>coords. >> >> cheers >> Bruce >> >> p.s. not sure why it would be smaller >> >> On Fri, 9 Sep 2011, Maria Felber wrote: >> >>> Dear all, >>> >>> sorry, if that question came up before in the mailing list and I >>>simple have been unable to find the thread. >>> >>> Following the wiki reconstruction workflow, I ran yesterday the >>>recon-all -all process. The process finished without errors. So the >>>next step was to check the talairach transform. >>> Now, according to the FsTutorial/Talairach I have to make some >>>adjustments and then run the whole process again. That is all nice and >>>good. >>> >>> However, why is it, that the talairach volume is always, no matter >>>which subject I look at, is always significantly smaller than the >>>target volume? Is that normal? Has it to be fixed? Or is that just >>>normal? Attached find one example. >>> As I am using freesurfer for the first time, I am really unsure about >>>that. >>> >>> Thanks for the help, >>> Maria >>> >>> >> >> >> 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. >> >> >> > >-- >Maria J. Felber, PhD Student >Max Planck Institute for Human Cognitive and Brain Sciences >Stephanstraße 1A >04103 Leipzig, Germany >Phone: +49 341 9940-2465/2522 > >-- >Maria J. Felber, PhD Student >Max Planck Institute for Human Cognitive and Brain Sciences >Stephanstraße 1A >04103 Leipzig, Germany >Phone: +49 341 9940-2465/2522 > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522

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