Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

having two freesurfer versions at one computer
by Tetiana Dadakova 06 Jul '11

06 Jul '11

Dear list, I would like to install both 5.0 and 5.1 versions on my computer. But I am not sure how exactly I should proceed after downloading the 5.1 (5.0 is already installed). For example, how should I set FREESURFER_HOME, can it be the same for both versions? Also, can I have my 5.0 in /Applications/freesurfer and 5.1 in /Applications/freesurfer5.1/freesurfer ? Thank you, Tanja.

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MRI registration
by Zeynep Akalin Acar 06 Jul '11

06 Jul '11

Hi all, I'm trying to register two brain volumes using Freesurfer. I need to find a mapping for each voxel of the MR image to the reference image. I tried using mri_register with the option -vf as the wiki documentation suggests that it outputs a vector field. Instead it expects a variance volume. The surface registrations do not work for me either, because they don't include a mapping of inner points. I tried Talairach transformation, but, it is a rigid registration, and I need a non-rigid registration. Is there a tool in Freesurfer that can register two brain volumes with a mapping of each voxel? Thanks, Zeynep.

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stats on masked functional data
by Ritobrato Datta 05 Jul '11

05 Jul '11

Hello All, I have a functional beta value overlay as a .mgh file and a label file and I want to compute the average value within that mask for each subject. Is there a program to do that ? Thanks Ri

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gyrification Index of a label
by Ritobrato Datta 05 Jul '11

05 Jul '11

Hi All, I have run recon-all -s <subj> -localGI Now I want to get the gyrification Index of a particular label. Is there a way to do that ? Please let me know Thanks Ri

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fieldsign problems
by Michelle Umali 05 Jul '11

05 Jul '11

Hi All, I am running a retinotopy analysis, and when I look at the fieldsign image all I see are a bunch of red and blue speckles. Is this normal? Thanks. Michelle

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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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Freesurfer July 2011