Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Cortical volume
by Wu, Mon-Ju 03 Oct '14

03 Oct '14

I have a quick question about FreeSurfer: is cortical volume the product of cortical thickness and cortical surface are? Conceptually I assume that to be the case, and I found several papers to support that. However, when I tried it with my own data, that seems to disagree with ~12% error. So I took a deeper look from your website and use the data from your following page as a test: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI_tktools (#StructName/ SurfArea/ GrayVol/ ThickAvg/ Surface*Thick) (bankssts/ 1133/ 2693/ 2.331/ 2641) (caudalanteriorcingulate/ 805/ 2396/ 2.657/ 2139) (caudalmiddlefrontal/ 2205/ 6275/ 2.528/ 5574) (cuneus/ 1597/ 3129/ 1.806/ 2884) (entorhinal/ 403/ 1837/ 3.268/ 1327) The above results are took directly from your website and the last column is the product of the surface are and thickness (calculated by me), Theoretically the Gray volume should agree with the product of surface area and the thickness. However, the results above showed about 10.8% error. So I was wondering is my hypothesis of "cortical volume is the product of cortical surface area and cortical thickness" wrong or am I missing something here? What should the relationship be between cortical surface area, cortical thickness, and cortical volume?

2 1

mri_glmfit and volume visuals‏
by Taylor North 03 Oct '14

03 Oct '14

Hello Freesurfer community, I am using the mri_glmfit model to analyze my group data at two time points. First I ran the following commanded swapping pc1 with spc to get an image of the symmetrized percent change across my group. ------------------------------------------------------------------------------------------------------------------------- long_mris_slopes --qdec long.testretest.qdec \ --meas thickness \ --hemi lh \ --sd $SUBJECTS_DIR \ --do-pc1 --do-label \ --generic-time \ --fwhm 15 \ --qcache fsaverage \ --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ --isec-labels lh.testretest.fsaverage.cortex.label mri_glmfit --osgm \ --glmdir lh.testretest.thickness-pc1.fwhm15 \ --y lh.testretest.thickness-pc1.stack.fwhm15.mgh \ --label lh.testretest.fsaverage.cortex.label \ --surf fsaverage lh tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fwhm15/osgm/sig.mgh --------------------------------------------------------------------------------------------------------------------------------------- Next I ran the following command to get volume change results: ---------------------------------------------------------------------------------------------------------------------------------------- long_stats_slopes --qdec long.testretest.qdec \ --stats aseg.stats \ --meas volume \ --sd $SUBJECTS_DIR \ --do-pc1 \ --generic-time \ --stack-pc1 testretest.aseg-pc1.stack.txt mri_glmfit --osgm \ --glmdir testretest.aseg-pc1 \ --table testretest.aseg-pc1.stack.txt cat testretest.aseg-pc1/sig.table.dat ---------------------------------------------------------------------------------------------------------------------------------------------- The results from the volume command are all in a table which is useful however I was wondering if there also is anyway to get a visual picture of the percent volume changes like the first spc command provided? Also is there any command that can give you the percent change in global brain volume? Thanks for the help! Cheers, Taylor North

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Freesurfer and 3D true - IR sequences
by Domenico 03 Oct '14

03 Oct '14

Dear all, I have a set of 3D true IR volumes acquired on a Siemens Avanto Scanner 1.5T. The GM/WM contrast is very good and the images look better (from a neuroradiological point of you) than the classical 3D T1 we usually acquire. The sign of the images (that in this sequence could be <0) could be adjusted (for example using Matlab) so to maintain the intensity ratio between the structures. Do you think I could use them for a Freesurfer analysis? Unfortunately the subjects were acquired some time ago, before starting to use FreeSurfer and only this 3DT1 sequence was acquired. Thank you, Kind regards, Domenico

2 1

modeling linear and quadratic effects simultaneously
by Schweren, LJS (med) 02 Oct '14

02 Oct '14

Dear Freesurfer experts, A while ago I sent the question below to the FS mailinglist, but it was never answered... Would anyone be able to help me with this issue? Thank you very much in advance! Best wishes, Lizanne Dear Freesurfer experts, I am modelling multiple covariates (age, SES, nr of symptoms and nr of symptoms2) in one subject group. For the quadratic term I added a column in the fsgd-file. I want to visualize the effect of nr of symptoms, either their linear or their quadratic effects. I therefore made two contrasts: The effect of symptoms: 0 0 1 0 And the effect of symptoms2: 0 0 0 1 I would like to model these two effects together in one contrast, to visualize the total effect of symptoms. I tried the following contrast: 0 0 1 0 0 0 0 1 But the result is very different from the two individual contrasts. I get large (non-overlapping) clusters of significant effect in the two separate contrasts, but with the combined contrasts I get none. What would be the appropriate contrast if I want to visualize all regions with the effects of symptoms, including both linear AND quadratic effects? Thank you very much for your help Best wishes, Lizanne ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

2 1

Reporting longitudinal change (pc1)
by Tudor Popescu 02 Oct '14

02 Oct '14

Dear FS list (dear Martin), I have a 3 groups x 2 timepoints data set, and I did analyses in QDEC comparing my groups pairwise (2 at a time) in terms of the pre-to-post percentage change (pc1) in various surface-based metrics like thickness and area. Since a group contrast is a bit difficult for readers to interpret (it would read "where is the percentage change from pre to post greater for group 1 than for group 2?"), I am wondering what is, in fact, best to report, aside from showing images of the significant clusters. What commands would I have to use, exactly, to for instnace, compute the group means for pre and for post values for e.g. thickness, i.e. absolute values rather than differences? I think I only have the pc1's calculated, since if I select thickness (rather than thickness-pc1) in QDEC, it tells me it cannot find the smoothed files. Thanks!

2 1

represent and show the TRACULA outputs
by stdp82＠virgilio.it 02 Oct '14

02 Oct '14

Hi,what is the best way to represent and show the TRACULA outputs?I would use 3D rendering, reporting the ouput on structural image.I'm trying several option but the resolution and results are poorly satisfactory. Particularly, if I use free view and I upload the aparc+aseg+2mm.flt.nii or cortex as reference, I must modify the opacity to visualize the tract, but the quality is low. Is there a way to cut a window within the cortical redering to visualize the deep tract?Please, may you give me some suggestion?Thank you very much.Regards, Stefano

1 0

Re: [Freesurfer] problems with tracula pre-processing (bvecs)
by Barbara Kreilkamp 02 Oct '14

02 Oct '14

Dear all, What does this mean? That tracula is more robust when running it seperately for the tracts I am interested in? Thanks, Barbara On Mon, Sep 15, 2014 at 4:44 PM, Michele Cavallari < cavallari.michele(a)gmail.com> wrote: > errata corrige: it did work! I had to re-run the whole thing including > only that specific tract...and eventually it worked. > > On Fri, Sep 12, 2014 at 11:19 AM, Michele Cavallari < > cavallari.michele(a)gmail.com> wrote: > >> Tried...unfortunately it didn't improve >> >> On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson < >> Christopher.Watson(a)childrens.harvard.edu> wrote: >> >>> You can try just re-running "trac-prep -prior" and "trac-paths" for >>> the L uncinate and no other tracts >>> >>> On 09/11/2014 02:58 PM, Michele Cavallari wrote: >>> >>> So, I re-ran the case with the set reinit option. It "half" >>> worked!...in the sense that the new results show the left uncinate right, >>> but the right-side one is still a dot (see screenshot of the brain view >>> from the bottom). >>> Any further suggestion? >>> Thanks. >>> >>> [image: Inline image 2] >>> >>> >>> >>> >>> >>> On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari < >>> cavallari.michele(a)gmail.com> wrote: >>> >>>> Thanks! it's running... >>>> >>>> On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp < >>>> bakk.hbg(a)googlemail.com> wrote: >>>> >>>>> Hi Michele, >>>>> >>>>> Don't think there is anything wrong with the attached dmrirc.tutorial >>>>> file. >>>>> You definitely need to add the '-c' flag infront of the path to your >>>>> configuration file. >>>>> Right now it reads the path to your file as a flag, which is of course >>>>> not what you want. >>>>> >>>>> Best, >>>>> Barbara >>>>> >>>>> >>>>> >>>>> >>>>> On 11/09/2014 17:49, Michele Cavallari wrote: >>>>> >>>>> Hi Anastasia, >>>>> I am probably doing something wrong with the syntax of the dmrirc >>>>> file. >>>>> I get this error message >>>>> >>>>> trac-all -prior >>>>> /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial >>>>> >>>>> ERROR: flag >>>>> /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial >>>>> unrecognized >>>>> >>>>> -prior >>>>> /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial >>>>> >>>>> Could you please check the attached file? >>>>> >>>>> >>>>> On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki < >>>>> ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>> >>>>>> >>>>>> Thanks, Michele. Hard to tell what's causing this, perhaps a bit of >>>>>> distortion orbitofrontally. You may be able to fix this type of thing by >>>>>> reinitializing the tract reconstruction: Add "set reinit = 1" to your >>>>>> configuration file, set the pathlist to include only the left and right >>>>>> uncinate, and then rerun the -prior and -path steps of trac-all on this >>>>>> subject. >>>>>> >>>>>> On Wed, 10 Sep 2014, Michele Cavallari wrote: >>>>>> >>>>>> uploaded (and activated).Thanks! >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki < >>>>>>> ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>> >>>>>>> Hi Michele - The anatomical segmentation does look good, but >>>>>>> from the >>>>>>> screenshot the DWI data seems to be noisy in the orbitofrontal >>>>>>> area, which >>>>>>> may be affecting the uncinate. It's hard to tell just from one >>>>>>> slice. >>>>>>> >>>>>>> If you upload all the tracula output directories of this >>>>>>> subject (dmri, >>>>>>> dmri.bedpostX, dlabel, dpath) for me here, I'll take a look: >>>>>>> https://gate.nmr.mgh.harvard.edu/filedrop2/ >>>>>>> >>>>>>> Thanks! >>>>>>> a.y >>>>>>> >>>>>>> On Wed, 10 Sep 2014, Michele Cavallari wrote: >>>>>>> >>>>>>> Hi Anastasia,I completed the tracula processing. >>>>>>> By looking at the tractography results in the viewer I >>>>>>> noticed >>>>>>> that the uncinate >>>>>>> fasciculus is pretty small (see attached screenshot). It >>>>>>> actually appears as a small >>>>>>> blue dot. And the problem is both on the left and right >>>>>>> side. >>>>>>> The other tracts look >>>>>>> fine. I played with threshold, but the size didn't >>>>>>> increase. So, >>>>>>> I guess that something >>>>>>> wrong happened with the tractography of that particular >>>>>>> bundle. >>>>>>> I checked the aparc+aseg >>>>>>> output (attached): it seems right to me, but could you >>>>>>> please >>>>>>> double-check? >>>>>>> Let me also know if you have any suggestions, and if you >>>>>>> need >>>>>>> more information or output >>>>>>> files. >>>>>>> Best, >>>>>>> Michele >>>>>>> >>>>>>> Inline image 1 >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki >>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>> >>>>>>> Hi Ludy - If your gradient table is formatted in 3 >>>>>>> rows >>>>>>> you need to >>>>>>> either: >>>>>>> >>>>>>> 1. Convert it to 3 columns so you can use it with >>>>>>> the 5.3 >>>>>>> version of >>>>>>> tracula, which requires the gradient table to be >>>>>>> formatted >>>>>>> in columns >>>>>>> >>>>>>> OR >>>>>>> >>>>>>> 2. Download the tracula update that can use >>>>>>> gradient >>>>>>> tables formatted in >>>>>>> rows >>>>>>> >>>>>>> Hope this helps, >>>>>>> a.y >>>>>>> >>>>>>> On Thu, 4 Sep 2014, lshih(a)bidmc.harvard.edu wrote: >>>>>>> >>>>>>> > Hi, >>>>>>> > >>>>>>> > I was having similar errors as Michele Cavallari >>>>>>> regarding "error reading >>>>>>> /path/to/subject/dmri/dwi_frame," but I'm not sure >>>>>>> it's >>>>>>> related to my bvecs >>>>>>> file. I did try reconfiguring my bvecs file into >>>>>>> columns >>>>>>> instead of row just >>>>>>> in case, but that didn't solve the problem. It >>>>>>> really just >>>>>>> looks like it >>>>>>> can't find the dwi_frame file after the mri_concat >>>>>>> command. >>>>>>> > >>>>>>> > I am attaching my trac-all.log and config file. >>>>>>> > >>>>>>> > Running Freesurfer 5.3 on Macbook OS 10.7.5. The >>>>>>> bvecs >>>>>>> files were >>>>>>> generated after I converted my dicoms to nifti >>>>>>> using >>>>>>> dcm2niigui (GE >>>>>>> scanner). >>>>>>> > >>>>>>> > Can anyone tell me how dwi_frame is generated? >>>>>>> > >>>>>>> > >>>>>>> > Ludy >>>>>>> > >>>>>>> > This message is intended for the use of the >>>>>>> person(s) to >>>>>>> whom it may be >>>>>>> addressed. It may contain information that is >>>>>>> privileged, >>>>>>> confidential, or >>>>>>> otherwise protected from disclosure under >>>>>>> applicable law. >>>>>>> If you are not the >>>>>>> intended recipient, any dissemination, >>>>>>> distribution, >>>>>>> copying, or use of this >>>>>>> information is prohibited. If you have received >>>>>>> this >>>>>>> message in error, >>>>>>> please permanently delete it and immediately >>>>>>> notify the >>>>>>> sender. Thank you. >>>>>>> > >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>>> >>>>>>> >>>>>>> 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 >>>>>> >>>>>> >>>>>> 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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 >>>>> >>>>> >>>>> 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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 >>> >>> >>> 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 > > > 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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PhD position | Technische Universität München, Munich, Germany
by Righart, Ruthger 02 Oct '14

02 Oct '14

PhD position in multiple sclerosis research Department of Neurology, Technische Universität München, Munich, Germany TUM-NIC, Neuroimaging Center, Munich, Germany The Department of Neurology of the Technische Universität München offers a PhD position in systems neuroscience research of Multiple Sclerosis. The project aims to investigate structural correlates of disability and biomarker patterns in patients with multiple sclerosis (MS) using MR imaging techniques. The candidate will investigate cortical pathology and lesion pathology in MS using state-of-the-art neuroimaging techniques. Applicants should have finished a university degree in medicine, psychology, biology, computer science or other relevant disciplines. Candidates should have strong analytical and organizational skills and prior experience with large cohort patient datasets is an advantage. Previous experience in analysis of structural/functional MR images (e.g., Freesurfer/FSL, SPM) is highly desired. Basic programming skills in for example Matlab or Unix shell scripting are a plus but not strictly required. Candidates who lack the aforementioned skills should have a strong motivation to develop these skills during their training. We are searching for candidates who are able to work independently and who have demonstrated excellent presentation and writing skills. The applicant will be expected to interact and collaborate with colleagues from different disciplines. Salary is according to the German TVöD. The position is available from January. The position is initially available for two years, the second year contingent on satisfactory progress. Extension beyond two years may be possible. Neuroimaging scanning facilities (MRI 3T scanner) and computer infrastructure are entirely available at the TUM Neuroimaging Center (TUM-NIC). Candidates may contact Prof Dr. Mark Mühlau (muehlau(a)lrz.tum.de) or Dr. Ruthger Righart (righart(a)lrz.tum.de) for more detailed information. Applications including a letter of motivation and CV should be addressed to Prof. Dr. Mühlau by Email: muehlau(a)lrz.tum.de .

1 0

Input files format
by Svetlana Soloveva 02 Oct '14

02 Oct '14

Dear all, If I understand correctly, it is recommended to use original MRI files as an input. However, I have only *.mri file. First, I was able to run reconstruction following fieldtrip pipeline which includes some preprocessing of *.mri and writing resulting files in *.mgz format that can be used by Freesurfer. Is there any other way to work with *.mri files in Freesurfer without these preprocessing steps? Many thanks! Svetlana

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White matter and white matter lesions
by Leise Borg 01 Oct '14

01 Oct '14

Hi FreeSurfer I am working on a project concerning Alzheimer's patients and I need to know the positions of white matter (WM) and white matter lesions (WML) from your segmentations. To find the WML, I use label 77 in the aparc.a2009s+aseg.mgz-files. To find the WM, I use labels 2 and 41 in the ribbon.mgz-files and subtract the ventricles by subtracting labels: 4, 5 14, 15, 43 44 found in the aseg.mgz-files. However, in the two sets of positions - one for WML and one for WM -there is an overlap. It is not big, but it is there. Can you help me finding the true WML- and WM-segmentations? With kind regards, Leise.

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