Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

WM edit, remove GM bright rim
by Min Liu 16 Mar '16

16 Mar '16

Dear Freesufer users, We have some T1 images having a rim of bright signal in the GM at some spots like the one showing in the attached Figure 1. The WM surface goes out to include this bright signal and the cortex ends up artificially thin. We followed the standard WM edit procedure, which is to erase the bright signal in wm.mgz. As shown in Figure 2, the bright rim is replaced with intensity 1 (red). However, that doesn't improve the situation. Does anyone know a way to prevent the surface from going out? Thanks, -- Min

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Hippocampal subfield segmentation with T1&T2
by Zhuang, Xiaowei 16 Mar '16

16 Mar '16

Dear Freesurfer expert, I am using Freesurfer V6.0 beta version to run the hippocampal subfield segmentation with 2 inputs, a standard T1 and a high resolution T2. Below are the details about the 2 images. T1: resolution: 0.8*0.8*0.8 mm, orientation: Sagittal(S>T4.1>C-0.8) T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5). The instruction says in order to use both of them for hippocampal segmentation, T2 should be in the same orientation as T1. Therefore, the two images cannot be used directly. Is it possible for me to do some reorient preprocess on the T2 image and then run through the segmentation? Or is it possible to coregister the T1 into T2 space, making them both high resolution and run through the segmentation? Will this affect the Freesurfer pipeline and the final subfields output? Any suggestion will help. Sincerely thanks, Xiaowei. [Cleveland Clinic logo] Xiaowei Zhuang | Research Engineer | Lou Ruvo Center for Brain Health Cleveland Clinic | 888 W Bonneville Ave. | Las Vegas, NV 89106 | (702) 685-6051 =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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surface based analysis using FA maps
by Alshikho, Mohamad J. 16 Mar '16

16 Mar '16

Hi Doug, I would like to run surface based analysis using FA maps. I am not exactly sure that what I am doing is totally right specially step 2 . I used the following commands: 1. I registered the FA maps to T1 using the command: bbregister --s bert --mov dtifit_FA.nii --bold --init-fsl --reg reg.dat 2. I concatenated the subject's FA maps using the command : mris_preproc -target fsaverage -hemi lh -iv .bert1/dtifit_FA.nii reg.dat -iv bert2/dtifit_FA.nii reg.dat .... --projfrac 0.5 --out lh.FA.mgz 3. Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.FA.mgz --tval lh.FA_5mm.mgz 4. Then GLM analysis using mri_glmfit 5. Correction for multiple comparison mri_glmfit-sim Kindly, are these steps correct? I highly appreciate any input on this! Best, Mohamad

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FWHM file not found
by Pedro Rosa 16 Mar '16

16 Mar '16

Dear FreeSurfers, I am running a localgi analysis using mri_glmfit and mri_glmfit-sim, and it seems the last script looked for freesurfer/average/mult-comp-cor/fsaverage/?h/cortex/fwhm40/abs/th13/mc-z.cdf and mc-z.csd, but there are precached data until fmhm30. How should I proceed? Best, Pedro.

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Re: [Freesurfer] group analysis all measures same results
by Douglas N Greve 16 Mar '16

16 Mar '16

this only has to do with the qcache part of recon-all, so you could use version 5.3 recon-all -qcache and it should be fine. However, it is not a good idea to try to publish using the analysis from the version of FS that you used. That was a beta version of version 6 and things will change. On 03/15/2016 01:56 PM, Kaiming Yin wrote: > Dear Douglas, > > Is there anything I can do now to fix this now? I don't want to re-run > all the data again. > > Thanks, > Kaiming > > > On 15 March 2016 at 16:53, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > OK, this is a bug that I found and fixed in early Nov. Sorry, > that's part of the danger of using a beta version. > > On 03/14/2016 12:22 PM, Kaiming Yin wrote: > > Dear Douglas, > > I re-run the "-qcache" on one data and it took 8 mins to > finish. Still the files are the same, all in 668.6kB size. > > > Kaiming > > On 14 March 2016 at 15:56, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > I don't know what happened. I cannot replicate it here. > Can you > re-run the recon-all -s -qcache command and verify that > the files > are still the same? > > > On 3/14/16 11:11 AM, Kaiming Yin wrote: > > Dear Douglas, > > Yes, both of the two pairs of files are the same. i.e. > > mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh > > diffcount 0 > > > mri_diff rh.thickness.fwhm10.fsaverage.mgh > rh.area.fwhm10.fsaverage.mgh > > diffcount 0 > > > Does this mean I run the "-qcache" wrongly? I just run > "recon-all > -s XX -qcache" on each subject. > > Thanks, > Kaiming > > > On 14 March 2016 at 14:58, Douglas Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Check whether rh.ad_hv.thick.10.mgh and > rh.ad_hv.area.10.mgh > are the same, ie, > mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh > > If those are the same, then check whether > thickness.fwhm10.fsaverage and > area.fwhm10.fsaverage are the > same in each subject > > > On 3/14/16 10:53 AM, Kaiming Yin wrote: > > Dear Douglas, > > My command lines were, e.g. right thickness > and right white > surface (using the same ad_hv.fsgd and > group_diff.mtx files > in the command lines): > > > ad_hv.fsgd > > GroupDescriptorFile 1 > Title AD_HV_GroupAnalysis > Class AD > Class HV > InputAD_003AD > InputAD_005AD > ... > InputHV_ABHV > InputHV_AEHV > > > group_diff.mtx > > 1 -1 > > > right thickness > > mris_preproc --fsgd ad_hv.fsgd --cache-in > thickness.fwhm10.fsaverage --target fsaverage > --hemi rh > --out rh.ad_hv.thick.10.mgh > > mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd > ad_hv.fsgd dods > --C group_diff.mtx --surf fsaverage rh > --cortex --glmdir > rh.ad_hv.thick.glmdir > > mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir > --cache 4 neg > --cwp 0.05 --2spaces > > > right white surface > > mris_preproc --fsgd ad_hv.fsgd --cache-in > area.fwhm10.fsaverage --target fsaverage > --hemi rh --out > rh.ad_hv.area.10.mgh > > mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd > ad_hv.fsgd dods > --C group_diff.mtx --surf fsaverage rh > --cortex --glmdir > rh.ad_hv.area.glmdir > > mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir > --cache 4 neg > --cwp 0.05 --2spaces > > > Their results were all the same. > > Thanks, > Kaiming > > > ---------- Forwarded message ---------- > From: Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > To: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Cc: > Date: Mon, 7 Mar 2016 18:47:11 -0500 > Subject: Re: [Freesurfer] group analysis all > measures same > results > what are your command lines? > > > On 5 March 2016 at 02:01, Kaiming Yin > <yinkaiming6987(a)gmail.com > <mailto:yinkaiming6987@gmail.com> > <mailto:yinkaiming6987@gmail.com > <mailto:yinkaiming6987@gmail.com>>> > > wrote: > > Dear guys, > > I was doing group analysis (command-line) > on two groups > (patients and control, no age or other > information). The > data has been "qcached", and after > following the three > steps as "mris_preproc, mri_glmfit and > mri_glmfit-sim" > shown in the tutorial on the Freesurfer > website, I > obtained the difference on thickness in > both left and > right hemispheres, which seems great. > However, when I > repeated the above steps on other > measures, e.g. area, > area.pial, volume (also replaced the parts of > "thickness" in the command lines), the > results seemed to > be exactly the same again as those in the > thickness > comparison, even the p-value numbers in > the file > "cache.th40.neg.sig.cluster.summary" were > the same. I > was using Freesurfer v6.0-beta, and I > performed the > individual data analysis on a linux > cluster and I > copied/downloaded the whole "qcached" > subject directory > to my linux laptop to perform the group > comparison, both > using the same version of Freesurfer, does > it matter? Or > do you know why it happened like this? > > Thanks, > Kaiming > > > > 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. > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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LUT in ImageJ
by Kaiming Yin 16 Mar '16

16 Mar '16

Dear guys, Is there a file of "FreeSurferColorLUT.txt" available in the Freesurfer folders, or should I copy/paste the texts to a .txt file directly from the FS website? Also, is there a way to transform this LUT table to enable it to be loaded into ImageJ, or can it work directly well in ImageJ? Thanks, Kaiming

2 1

Smoothing at FWHM (Qdec)
by Martin Juneja 16 Mar '16

16 Mar '16

Hello everyone, I am very new to FreeSurfer. Although I know what smoothing means etc. but I am not sure what smoothing level is the best to choose while comparing cortical thinning for patients vs. controls. Qdec gives several options to choose from among 0, 5, 10, 15, 20 and 25. Literature says 10 mm is the typical value to choose but when I calculate clusters, I don't see any significant clusters (at FDR p < 0.05) but at smoothing level 20 mm, I can see several clusters at the same threshold i.e. at FDR p < 0.05. I would really appreciate if someone, expert in this field could guide me regarding this. Also, may be if someone could recommend me a few papers from literature discussing this issue e.g. effect of smoothing on cortical thickness etc., that would be very useful. Thanks, MJ

2 1

mri_fwhm
by John Anderson 16 Mar '16

16 Mar '16

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Problems with file un qdec analysis
by Lisa Delalande 16 Mar '16

16 Mar '16

Hello everyone, I've got some problems with qdec. I have .levels with more than 2 factors. For example a "grpe.levels" with three factors : children (enfant), adults (adultes) and nothing (rien). But if I want to exclude some subjects like children qdec doesn't work anymore (attachment : error message). Is that possible a .levels can not have more than two factors ? Or the problem came from anything else ? Thanks in advance for your help ! Best regards, Lisa

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Anterior to Posterior Length
by Heather Acuff 16 Mar '16

16 Mar '16

Good morning, I apologize if this email was sent out twice. I would like to use anterior to posterior length as a covariate in my DTI analysis. Is there an easy way to obtain this information for each subject? Thank you, Heather

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