Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

mri_glmfit with diffusion data
by Lilla Zollei 12 Aug '11

12 Aug '11

Hi, I have some diffusion scans acquired at the Childrens and when running mri_glmfit on them to reconstrct the tensors, I get the following error. "ERROR: cannot extract sDiffusion.alBValue[1] from dwi-infodump.dat" I checked the dump file and there is a field sDiffusion.alBValue[0]. Does that contain the same information? If I modify my local version of the code to read that value in, then the error message is about "ERROR: cannot extract sWiPMemBlock.alFree[8] from dwi-infodump.dat" I am not really sure how to find the correct value for that as there is nothing similar to it in the dump file. Any ideas?

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Re: [Freesurfer] FreeSurfer result wrong without error during process
by Tali Swisher 12 Aug '11

12 Aug '11

Hi all, I have a case whose resulting wmparc.mgz is completely misaligned from the brain, and is much smaller than it should be. The case ran fine, however, and I received no error messages at any point. Any ideas? Thanks! Tali On Fri, Aug 12, 2011 at 10:39 AM, Tali Swisher <tali(a)bwh.harvard.edu> wrote: > Hi all, > > I have a case whose resulting wmparc.mgz is completely misaligned from the > brain, and is much smaller than it should be. The case ran fine, however, > and I received no error messages at any point. Any ideas? I've attached the > wmparc.mgz, brain.mgz, and the recon-all.log. > > Thanks! > Tali > > > -- > Talis M. Swisher, BA > Research Assistant > Psychiatry Neuroimaging Laboratory > Harvard Medical School, Brigham and Women's Hospital > 1249 Boylston St, 3rd Floor > Boston, MA 02215 > Office: (617) 525-6119 > Cell: (336) 577-5071 > Fax: (617) 525-6150 > > -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150

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Re: [Freesurfer] Label2label on fsaverage
by Rouhollah Abdollahi 12 Aug '11

12 Aug '11

Dear Bruce, I have two questions. I saw there are a lot of algorithms for mris_register. Which one are more precise and has less distortion on sulci pattern? In initial alignment if I want to rotate the surface with -rotate [ alpha is (ear to ear) beta(Back to nose) ... ]. Am I right?. and if I want that mris_register does not apply any rigid alignment after initial rotation what I have to do? Thanks Rouhi On Thu, Aug 11, 2011 at 9:25 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > What format is the attachment in? > > > > On Aug 11, 2011, at 8:32 PM, Rouhollah Abdollahi <roohy466(a)gmail.com> > wrote: > > Dear Bruce > I checked the parcellation and look quiet OK. I attached two subjects , > whcih subj_1 shows bad registration to fsaverage and subj_2 shows the good > registration. I attached a file which compare two subjects according to > sphere and sphere.reg. For the subj_1 , it has more figures to see how the > parcellation is. > Thanks in advance > > Best > Rouhi > > On Thu, Aug 11, 2011 at 10:48 AM, Bruce Fischl <<fischl(a)nmr.mgh.harvard.edu> > fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Rouhi >> >> check the parcellations. If they are correct then the sphere.reg must be >> pretty accurate. >> >> cheers >> Bruce >> >> On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >>> >>> I am working on Freesurfer 2 caret meshes. I am using ** >>> FreeSurfer2CaretConvertAndRegi**sterClean.sh from Van Essen lab to >>> create caret surfaces. when I look at my subjects' >>> surfaces I can see in flat map in caret some of subjects sulci patterns >>> are really distorted and I think it is related to sphere registration to >>> fsaverage sphere. Beacsue >>> the code is using sphere.reg to create all surfaces. for the subjects >>> which I have less distortion on sulci pattern I have good data (3 subjects) >>> but for the (9 subjects) >>> rest it seems they have problem to register to fsaverage. Is there any >>> way that I can be sure that sphere.reg properly created? >>> >>> Thank you very much >>> >>> Rouhi >>> >>> >>> >>> On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <<fischl(a)nmr.mgh.harvard.edu> >>> fischl(a)nmr.mgh.harvard.edu> wrote: >>> Try using fsaverage as the trgsubject >>> Cheers >>> Bruce >>> >>> >>> >>> On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <<roohy466(a)gmail.com> >>> roohy466(a)gmail.com> wrote: >>> >>> > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg >>> sphere.reg --hemi rh and when I tried to load the output label file on >>> fsaverage surface >>> like inflated one it shows a lot of point looks like it is not >>> deformed properly. Is it related to registration to fsaverage or something >>> esle? The question is >>> how I can register the subjects surfaces to fsaverage surfaces? -- >>> With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: >>> text/html; >>> charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear >>> freesurfer experts >>> > >>> > I've tried to export my label file from individual space to >>> fsaverage space by using this command: >>> > >>> > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 >>> --trgsubject SUB1 --trglabel rh.V1_reg. >>> > like it is not deformed properly. >>> > Is it related to registration to fsaverage or something esle? >>> > The question is how I can register the subjects surfaces to fsaverage >>> >>> >>> 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. >>> >>> >>> >>> >>> -- >>> With Best Regards >>> Rouhollah Abdollahi >>> >>> >>> >>> >>> > > > -- > With Best Regards > Rouhollah Abdollahi > > > > <subject_1&2_side_view.odp> > > -- With Best Regards Rouhollah Abdollahi

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Re: [Freesurfer] Label2label on fsaverage
by Bruce Fischl 12 Aug '11

12 Aug '11

Hi Rouhi it's hard to tell from looking at the sphere.reg by itself. In general though if the parcellations are correct then the registration must be pretty good. cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: > Dear Bruce > I checked the parcellation and look quiet OK. I attached two subjects , whcih subj_1 shows bad registration to fsaverage and subj_2 shows the > good registration. I attached a file which compare two subjects according to sphere and sphere.reg. For the subj_1 , it has more figures to see > how the parcellation is. > Thanks in advance > > Best > Rouhi > > On Thu, Aug 11, 2011 at 10:48 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Rouhi > > check the parcellations. If they are correct then the sphere.reg must be pretty accurate. > > cheers > Bruce > > On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: > > Dear Bruce > > I am working on Freesurfer 2 caret meshes. I am using FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create > caret surfaces. when I look at my subjects' > surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to > sphere registration to fsaverage sphere. Beacsue > the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good > data (3 subjects) but for the (9 subjects) > rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that > sphere.reg properly created? > > Thank you very much > > Rouhi > > > > On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Try using fsaverage as the trgsubject > Cheers > Bruce > > > > On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466(a)gmail.com> wrote: > > > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the > output label file on fsaverage surface > like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to > fsaverage or something esle? The question is > how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 > Content-Type: text/html; > charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts > > > > I've tried to export my label file from individual space to fsaverage space by using this command: > > > > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. > > like it is not deformed properly. > > Is it related to registration to fsaverage or something esle? > > The question is how I can register the subjects surfaces to fsaverage > > > 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. > > > > > -- > With Best Regards > Rouhollah Abdollahi > > > > > > > > -- > With Best Regards > Rouhollah Abdollahi > > > > >

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Flipping analyze images
by Catherine Wan 12 Aug '11

12 Aug '11

Dear List, I have a question regarding using .img in Freesurfer. We only have analyze images, but we can tell the orientation of the images through the patient's lesion location. Because freesurfer sometimes flips these image after recon-all, I'm now flipping the "problematic" ones using mri_convert <input> --out_orientation RAS <output> before running them again. Could someone please explain why if we use analyze images, some of them would be flipped by Freesurfer but not others? Does that only apply to lesioned/patient brains and not normal brains? Many thanks! Catherine

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nu_correct error
by Todd Krieg 11 Aug '11

11 Aug '11

To whom it may concern, I am having trouble running recon-all. I keep getting an error that nu_correct is not found. 'which nu_correct' return nothing. Here is the information: bugr output: FREESURFER_HOME: /home/mogul/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.35-22-generic x86_64 which recon-all /home/mogul/freesurfer/bin/recon-all Current working directory is ~ (/home/mogul) - aka root Command line ran: recon-all -s bert -autorecon1 Main error message received is: nu_correct: Command not found. ERROR: nu_correct recon-all.log file attached for additional information. I even uninstalled freesurfer and re-installed it with the same problem. Any help you could offer would be much appreciated. Thank you for your time. ---Todd Krieg tkrieg(a)hawk.iit.edu

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Brodmann areas stats table
by _andreia_＠sapo.pt 11 Aug '11

11 Aug '11

FreeSurfers, Is there a way to get BA cortical thickness in a table to export from FS? As there is for aseg and aparc stats. Thanks! Andreia -- Andreia Pereira, MSc student Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-354 Coimbra Portugal Phone +(351) 239480220 Fax +(351) 239480280

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Re: [Freesurfer] Volumetric analysis of thalamus in freesurfer
by Douglas N Greve 11 Aug '11

11 Aug '11

I'm not sure what you would visualize. These are just single numbers per subject. doug Knut J Bjuland wrote: > Hi > > Is is possible to visualize this data on sub-cortical structure in wya > similar to the aging tutorial? > > Knut J > > On 08/11/2011 09:03 PM, Douglas N Greve wrote: > >> use --segno 10 --segno 49 >> These codes are from $FREESURFER_HOME/FreeSurferColorLUT.txt and >> correspond to left and right thalamus. Use -m volume to get the volume >> of thalamus (this is the default). If you're only looking at one >> measure, then no correction for multiple comparisons is necessary. You >> can test the effect of gender by loading this output into a stats >> program or using mri_glmfit with the --table option. >> doug >> >> Knut J Bjuland wrote: >> >>> Hi Bruce >>> >>> I am now responding to the list as well. I have a group with different >>> subjects where I wish to correlate thalamus volume with gender >>> difference. Though I have extract the data using asegstats2table. I wish >>> to be sure that the group difference is correct. Due to this reason I >>> wish to use multiple comparsion within Freesurfer for instant FDR. I >>> have some trouble figuring out --iv volmeasfile or how to use an label >>> to include thalamus but exclude everything else? >>> >>> Knut J >>> >>> >>> Knut J >>> >>> On 08/11/2011 08:42 PM, Bruce Fischl wrote: >>> >>> >>>> Hi Knut >>>> >>>> you should respond onlist so Doug and Nick can answer! If all you want >>>> is thalamic volume then why do you have multiple comparisons? You only >>>> have one number/subject, no? >>>> Bruce >>>> >>>> On Thu, 11 Aug 2011, Knut J Bjuland wrote: >>>> >>>> >>>> >>>>> Hi Bruce >>>>> >>>>> I wish to use a group difference analysis using gender and correlate >>>>> thalamus volume with IQ, and then apply multiple comparisons using FDR >>>>> or Monte Carlo simulation. Do you have any links to a good tutorial? I >>>>> inted to use mris_preproc and mris_glm for voulmetirc analysis, but I >>>>> have some trouble figuring out --iv volmeasfile? >>>>> >>>>> Cheers >>>>> Knut J >>>>> >>>>> >>>>> Knut J >>>>> >>>>> On 08/11/2011 08:03 PM, Bruce Fischl wrote: >>>>> >>>>> >>>>>> Hi Knut >>>>>> >>>>>> you don't need to register it since the segmentation (aseg) is >>>>>> created >>>>>> from the same data as the surface. What kind of analysis are you >>>>>> thinking of doing? >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Thu, 11 Aug 2011, Knut J Bjuland wrote: >>>>>> >>>>>> >>>>>> >>>>>>> I am working to do a volumetric analysis in Freesurfer using >>>>>>> Thalamus. I >>>>>>> do not know if this is the correct way to go. Should I first >>>>>>> register >>>>>>> thalamus to a surface using tkregister? There was also another >>>>>>> post on >>>>>>> this list, which suggested using tkregister2? I am also search to >>>>>>> find >>>>>>> a tutorial on how to create a volmask and the use it to calculate >>>>>>> statistic in Freesurfer for Thalamus. >>>>>>> >>>>>>> Knut J >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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tksurfer & rtview
by Michelle Umali 11 Aug '11

11 Aug '11

Hi Doug, The z-values are consistently near or greater than 4. It just seems that the visualization of the angles is somehow incorrect... Is there be anything else that I need to check? Thanks. Michelle

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registration issues with lesioned brains and kids' brains
by Catherine Wan 11 Aug '11

11 Aug '11

Dear Freesurfer-list, I have 2 questions: one regarding lesioned brains and another regarding kids’ brains. 1) All of our patients have large lesions on the left side. After the recon-all step, I used tkmedit brainmask.mgz and found that for some patients, the lesion location had been flipped from left to right (see attached). Any suggestions on how to solve this issue, prior to running a group level analysis? 2) We have preprocessed some images of typically-developing children (9-11yo). After recon-all, I checked the registration using tkregister2 --mgz –s --fstal --surf orig and found that the green line didn’t cover the surfaces well in most cases (see attached) . I’ve read in previous postings that Freesurfer should be fine with kids’ brains, so perhaps we don't need to modify them manually? Is there any other way to check for registration? Any other suggestions? Many thanks in advance for your help! Regards, Catherine

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Freesurfer