Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Tksurfer Time Course Correlation
by Tyler Blazey 05 Jul '11

05 Jul '11

Hi, I have a couple of questions about Tksurfer's time course correlation option. First, what type of correlation does it show? Does it use Pearson's r or something else? Second, is there any way to get the same output from the command line? From previous list discussions, it looks like it might be possible using a Tcl script, but I am looking for more of a standard unix/linux command. Thanks for any help, - Tyler

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Re: [Freesurfer] Thickness measurements stats
by Bruce Fischl 05 Jul '11

05 Jul '11

Hi Ignacio, the thickness is definitely affected by factors such as sequence type, field strength and acquisition parameters (not to mention age, maybe gender, etc...) so I think you need to acquire your own control(s) on a matched acquisition. cheers. Bruce On Tue, 5 Jul 2011, Ignacio Letelier wrote: > Hi Bruce, > > Otherwise, is it possible to simply compare my T1 brain acquisition (with > dysplasia suspicion) with a 'normal template' (which maybe bert) to > determine whether there exist any anomaly in the cortical thickness ? and, > is it possible to visualize these potential differences using a color map > scaling? > > Thanks in advance- > > Best regards. > > Ignacio. > > 2011/7/3 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Ignacio, > > I see. You could do that, but I don't think it will show what > you want. There is a big geometric component to the thickness - > crowns are thick and fund are thin - so at the very least you > might try including mean curvature as a covariate. > > > cheers > Bruce > > On Fri, 1 Jul 2011, Ignacio Letelier wrote: > > Sorry I didn't realize since you have the same domain. > > Ok, Let's say I do know the mean cortical thickness value > of a subject. Then > is it possible know what brain areas differ more from > that mean value by > using a color map visualization (I.e. for example: red = > higher deviations, > deep blue = lower deviations)? So this way I can determine > where there may > exist some kind of dysplasia. > > Best regards. > > 2011/7/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > can you post this kind of thing so others can answer? > I still > don't understand though. stdv of what? > > > On Fri, 1 Jul 2011, Ignacio Letelier wrote: > > Let's say I want to know if there is a way to know > where > is the highest stdv in the same subject, using a > color map > visualization in qdec or something? > > Best regards. > > 2011/7/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Ignacio > > you mean different from the median in that > subject? > Easy enough to do in matlab, but we don't have > anything > out of the box to do it > > cheers > Bruce > > On Fri, 1 Jul 2011, Ignacio Letelier wrote: > > Hi forum > > Is it possible to get statistical maps of > cortical > thickness differences in the same subject? I.e. to > know > what areas differ most from the median > > > -- > Ignacio > > > > > 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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correct mris_anatomical_stats syntax for lgi
by ZhiLiangLong 05 Jul '11

05 Jul '11

Hi FS experts: I have run a group analysis with Local Gyrification Index (LGI) and obtained some statistical significant areas.Now I want to extract the information (lgi) of each area.Based on the QDec Group Analysis page, the following command is ran to examine cortical thickness: mris_anatomical_stats -l rh.test.label -t rh.thickness -b -f subject/stats/rh.test.stats subject rh Is it possible that i can adjust this for lgi ? If so,would i just replace the rh.thickness above with rh.pial_lgi ? many thanks for any help!

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Re: [Freesurfer] error using recon-all function
by Ryan Hutten 05 Jul '11

05 Jul '11

Freesurfer experts, I emailed last week with an error using recon-all. This problem has still not been resolved. The summary of the problem should be shown below: Thanks, Ryan On Fri, Jul 1, 2011 at 2:06 PM, Ryan Hutten < ryanhutten2012(a)u.northwestern.edu> wrote: > > > ---------- Forwarded message ---------- > From: Ryan Hutten <ryanhutten2012(a)u.northwestern.edu> > Date: Thu, Jun 30, 2011 at 1:34 PM > Subject: Re: [Freesurfer] error using recon-all function > To: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> > > > Krish, > > under the $FREESURFER_HOME/bin directory, there is a file named avi2talxfm > > I copied the output of the command you sent me. > > > tar -ztvf freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz | grep > avi2tal > -rwxr-xr-x root/root 2087 2011-05-22 08:28 freesurfer/bin/avi2talxfm > > > It looks like the file is there, but something is not working with it. Any > ideas? > > Thanks, > Ryan > > > On Thu, Jun 30, 2011 at 12:53 PM, Krish Subramaniam < > krish(a)nmr.mgh.harvard.edu> wrote: > >> Hi Ryan >> >> We do bundle avi2talxfm in our distribution. Can you see that in >> $FREESURFER_HOME/bin ? >> >> If you have the original freesurfer download file.. can you do a >> >> tar -ztvf freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0.tar.gz | >> grep avi2tal >> >> and see if it can find in the distribution ? >> >> Krish >> >> >> On 06/30/2011 01:35 PM, Bruce Fischl wrote: >> >>> I assume you have to install it. Nick or Krish? >>> On Thu, 30 Jun 2011, Ryan Hutten wrote: >>> >>> Is this something that I can add manually to one of the files? Please >>>> let me know what steps I can take to correct this problem. >>>> >>>> Thanks, >>>> Ryan >>>> >>>> On Wed, Jun 29, 2011 at 1:22 PM, Bruce Fischl < >>>> fischl(a)nmr.mgh.harvard.edu> wrote: >>>> Nick: it looks like he's missing this command: >>>> >>>> >>>> tail ~/talairach_avi.log >>>> Reading: /usr/local/freesurfer/average/** >>>> 711-2C_as_mni_average_305.**4dfp.ifh >>>> Writing: talsrcimg_to_711-2C_as_mni_**average_305_t4_vox2vox.txt >>>> >>>> start time Wed Jun 29 13:05:58 CDT 2011 >>>> end time Wed Jun 29 13:06:19 CDT 2011 >>>> >>>> mpr2mni305 success >>>> >>>> avi2talxfm orig.mgz /usr/local/freesurfer/average/**mni305.cor.mgz >>>> talsrcimg_to_711-2C_as_mni_**average_305_t4_vox2vox.txt >>>> transforms/talairach.auto.xfm >>>> avi2talxfm: Command not found. >>>> >>>> >>>> On Wed, 29 Jun 2011, Ryan Hutten wrote: >>>> >>>> I have attached the talairach_avi.log file. >>>> >>>> Thanks, >>>> Ryan >>>> >>>> On Wed, Jun 29, 2011 at 1:18 PM, Bruce Fischl < >>>> fischl(a)nmr.mgh.harvard.edu> wrote: >>>> Hi Ryan, >>>> >>>> what is in transforms/talairach_avi.log? >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> >>>> On Wed, 29 Jun 2011, Ryan Hutten wrote: >>>> >>>> > Hi, >>>> > >>>> > I am currently trying to use the recon-all function. It works fine on >>>> an older computer, but my group is attempting to get freesurfer up and >>>> running on >>>> a newer computer. The subject >>>> data is >>>> > located in a folder called 2645166 as shown in the following command. >>>> > >>>> > When I run the command: >>>> > >>>> > recon-all -s 2645166 -all >>>> > >>>> > I get the following error after the script runs for about a minute: >>>> > >>>> > ERROR: avi2talxfm failed, see transforms/talairach_avi.log >>>> > Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC >>>> 2010 x86_64 x86_64 x86_64 GNU/Linux >>>> > >>>> > >>>> > The output of your bugr script gives: >>>> > FREESURFER_HOME: /usr/local/freesurfer >>>> > >>>> > Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 >>>> > >>>> > RedHat release: Fedora release 14 (Laughlin) >>>> > >>>> > Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64 >>>> > >>>> > >>>> > A brief internet search found nothing regarding this avi2talxfm >>>> function. Any suggestions and/or help would be greatly appreciated. >>>> > >>>> > Thanks, >>>> > >>>> ______________________________**_________________ >>>> Freesurfer mailing list >>>> 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. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >> > >

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Fwd: freesurfer recon error
by Sarah Rappaport - UoB` 05 Jul '11

05 Jul '11

Hi!, I am new to FreeSurfer and I am having some difficulty with the T1 reconstruction. My MRI files were Par Rec and converted to nii. I successfully converted the nii file to mgz but had errors when running the recon -all command (see screen print attached). I have tried re-exporting the files in case there was an inital error at this stage but it returned the same error. I would appreciate any help with this. thanks Sarah

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Re: [Freesurfer] Display data for Cortical thickness
by Bruce Fischl 04 Jul '11

04 Jul '11

Hi Antonella, those regions should be compiled in the stats/aparc.annot.ctab file that should be easy to import into excel or other packages for analsys and plotting. cheers Bruce On Mon, 4 Jul 2011, Antonella Kis wrote: > > > Good morning Bruce, > > I posted my message also to the list and I will appreciate any help I can > get ASAP. > > I used freesurfer (v.5.1.0) on one subject using the MRI data and I finished > the recon-all step and qcache -all. I was able to display the thickness map > but I would like to get a quatitative measure of cortical thickenss for my > subject for the 34 neuroanatomical regions per hemisphere(4 medial temporal, > 5 lateral temporal, 11 frontal, etc) and display this data in a table where > I want to include the number of vertices and the cortical tickness for > different regions: > > > > caudalanteriorcingulate, > caudalmiddlefrontal, > cuneus > entorhinal > fusiform > inferiorparietal > inferiortemporal > isthmuscingulate > lateraloccipital > lateralorbitofrontal > lingual > medialorbitofrontal > middletemporal > parahippocampal > paracentral > parsopercularis > parsorbitalis > parstriangularis > pericalcarine > postcentral > posteriorcingulate > precentral > precuneus > rostralanteriorcingulate > rostralmiddlefrontal > superiorfrontal > superiorparietal > superiortemporal > supramarginal > frontalpole > temporalpole > transversetemporal > insula > > MiddleFrontal > InferiorFrontal > OrbitoFrontal > FrontalLobe > CingulateCortex > MedialTemporal > LateralTemporal > Parietal > Occipital > Region R > unknown > bankssts > caudalanteriorcingulate > caudalmiddlefrontal > cuneus > entorhinal > fusiform > inferiorparietal > inferiortemporal > isthmuscingulate > lateraloccipital > lateralorbitofrontal > lingual > medialorbitofrontal > middletemporal > parahippocampal > paracentral > parsopercularis > parsorbitalis > parstriangularis > pericalcarine > postcentral > posteriorcingulate > precentral > precuneus > rostralanteriorcingulate > rostralmiddlefrontal > superiorfrontal > superiorparietal > superiortemporal > supramarginal > frontalpole > temporalpole > transversetemporal > insula > > MiddleFrontal > InferiorFrontal > OrbitoFrontal > FrontalLobe > CingulateCortex > MedialTemporal > LateralTemporal > Parietal > Occipital > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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be derived from an automated labeling system tha > t subdivides the cerebral cortex on volumetric MRI > into 34 neuroanatomical regions per hemisphere. > I don't know how to do this so would you advise/teach me please? > Many thanks for your valuable help! > Antonella > ------------------------------ > > ____________________________________________________________________________ > > This e-mail may contain confidential, personal and/or health > information(information which may be subject to legal restrictions on use, > retention and/or disclosure) for the sole use of the intended recipient. Any > review or distribution by anyone other than the person for whom it was > originally intended is strictly prohibited. If you have received this e-mail > in error, please contact the sender and delete all copies. > >

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PET analyses in cortical regions
by Joao Pereira 04 Jul '11

04 Jul '11

Dear Freesurfers, My goal is to evaluate the cortical thinning patterns in some (cortical aparc) regions, and to relate that to loss of PET activation in the same regions. I would like to clarify the steps of the pipeline in Freesurfer (v5.0.0) for this purpose. >From my reading of previous discussions in the mailing list, I can see two possible ways of doing this - but I am not sure and I would like to ask for your feedback on them: First method: 1) Register all PET scans (already in ICBM152 space, enforced with SPM8) to the brain.mgz image of each subject to ensure the PET files are in MNI305 space, to be able to use Freesurfer's atlas, using bbregister or spmregister. 2) Use mri_vol2surf to project the PET data onto the surface of each subject. 3) Use mri_segstats to extract the statistics for each region. Second method: 1) (Same as above). 2) Use mri_annot2label on the relevant aparc regions. 3) Use results from the previous step in mri_label2vol to create the volume masks extracted from the cortical regions. 4) Apply mri_segstats on these (as above). Could you please clarify if I am on the right track, notably which method should be more robust (or correct...)? Also, does mri_segstats also give overall group statistics (mean, std) for each region, or must I use another function/average all subjects together for that? Thank you very much! Best, Joao Pereira Wolfson Brain Imaging Centre University of Cambridge

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Creating a ROI mask
by leonardo kay 04 Jul '11

04 Jul '11

Hi freesurfer 's Can anyone help me how to create a ROI mask. I have read the Cortical Thickness of a Volume-defined ROI tutorial but it doesn't specify how to generate that ROI.nii file. How many points are needed? What brain image must be used as a reference? Any help will be greatly appreciated Best regards. -- Leo Kay.

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Display data for Cortical thickness
by Antonella Kis 04 Jul '11

04 Jul '11

Good morning, I used freesurfer (v.5.1.0) on one subject using the MRI data and I finished the recon-all step and qcache -all. I was able to display the thickness map but I would like to get a quatitative measure of cortical thickenss for my subject for the 34 neuroanatomical regions per hemisphere(4 medial temporal, 5 lateral temporal, 11 frontal, etc) and display this data in a table where I want to include the number of vertices and the cortical tickness for different regions: caudalanteriorcingulate, caudalmiddlefrontal, cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula MiddleFrontal InferiorFrontal OrbitoFrontal FrontalLobe CingulateCortex MedialTemporal LateralTemporal Parietal Occipital Region R unknown bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula MiddleFrontal InferiorFrontal OrbitoFrontal FrontalLobe CingulateCortex MedialTemporal LateralTemporal Parietal Occipital I believe the thickness data is stored in lh. thickness and I should be able to read it in matlab but I am not very shure how. Also I want to estimate the cortical thickness for gyral based regions of interest ROIs. The gyral-based ROIs should be derived from an automated labeling system that subdivides the cerebral cortex on volumetric MRI into 34 neuroanatomical regions per hemisphere. I don't know how to do this so would you advise/teach me please? Many thanks for your valuable help! Antonella ------------------------------ ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Re: [Freesurfer] Thickness measurements stats
by Ignacio Letelier 03 Jul '11

03 Jul '11

Sorry I didn't realize since you have the same domain. Ok, Let's say I do know the mean cortical thickness value of a subject. Then is it possible know what brain areas differ more from that mean value by using a color map visualization (I.e. for example: red = higher deviations, deep blue = lower deviations)? So this way I can determine where there may exist some kind of dysplasia. Best regards. 2011/7/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > can you post this kind of thing so others can answer? I still don't > understand though. stdv of what? > > > On Fri, 1 Jul 2011, Ignacio Letelier wrote: > > Let's say I want to know if there is a way to know where is the highest >> stdv in the same subject, using a color map visualization in qdec or >> something? >> >> Best regards. >> >> 2011/7/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Ignacio >> >> you mean different from the median in that subject? Easy enough to do >> in matlab, but we don't have anything out of the box to do it >> >> cheers >> Bruce >> >> On Fri, 1 Jul 2011, Ignacio Letelier wrote: >> >> Hi forum >> >> Is it possible to get statistical maps of cortical thickness >> differences in the same subject? I.e. to know what areas differ most from >> the median >> >> >> -- >> Ignacio >> >> >> >> >> 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. >> >> >> >>

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