[Freesurfer] Global mean FA

Hi Dear Fs Experts I will post my question again, hopefully I can find an answer :) In order to calculate the global white matter fractional anisotropy FA I used (wm.mgz ) the output of recon-all as a mask in the following command line mri_segstats --seg $SUBJECTS_DIR/015601/mri/wmparc.mgz --cta

[Freesurfer] Deep white matter parcellated atlas

Hi Dear Fs Experts, I am looking for an atlas segmented all white matter without to leave any unsegmented white matter like in WMPARC I highly appreciate your help and support Thanks Mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu ht

[Freesurfer] Cerebellum white matter mask {Disarmed}

Hi Fs expers, What is the best way in Freesurfer to create a mask for the cerebellum white matter from the output of T1 segmentation? Thanks mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/lis

Re: [Freesurfer] Cerebellum white matter mask {Disarmed}

the aseg.mgz. cheers Bruce On Mon, 28 Jul 2014, Alshikho, Mohamad J. wrote: > Hi Fs expers, What is the best way in Freesurfer to create a mask for the > cerebellum white matter from the output of T1 segmentation? > > > T

Re: [Freesurfer] Cerebellum white matter mask {Disarmed}

{Disarmed} With mri_binarize you can give it multiple match options to merge different segments On 07/28/2014 11:50 AM, Alshikho, Mohamad J. wrote: > Hi Bruce, > Thank you very much for your quick answer, > The output of those command lines are left and right cerebellum white matter. &g

[Freesurfer] The difference between wm.mgz and wm.seg.mgz

Dear Fs Experts, What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres and brain stem except the cerebellum) Thanks Mohamad ___ Freesurfer mailing list Fre

Re: [Freesurfer] FW: The difference between wm.mgz and wm.seg.mgz

works really well (so well that the MJ ported it to FSL!) cheers Bruce On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote: > Thanks, Actually I tried to create a mask for the cerebellum using > mri_binarize --i aseg.mgz --o cerebellum.mgz --match 7 46 . Then I re > positioned this ma

[Freesurfer] mri_binzrize (flag --wm )

Hi, I have a question about the flag " -wm" in mri_binarize: The following segments IDs 8 2 41 82 251 252 253 254 255 are included in this flag (based on the summary of this command line when I run it). Kindly what is the segment ID (Right-non-WM-hypointensities) means? and why the (left-non-WM-

Re: [Freesurfer] mri_binzrize (flag --wm )

es are hypointense voxels (in T1 images) in > the right hemisphere in regions that are not normally white matter > (like the middle of the putamen). > > I'll leave your other questions for Doug > > cheers > Bruce > > > On Wed, 30 Jul 2014, Alshikho, Mohamad J. wrote:

[Freesurfer] Righty and left hemispheric white matter volume

Dear FS Experts, I am beginner in FS and I need you precious advice... In order to compare the volume of the right and left hemispheric white matter in my dataset (29 controls 23 patients). I did recon_all for my T1 data then I used the volume of the Left and right cerebral white matter which a

Re: [Freesurfer] T1 white matter segmentation

subsequent invocation of recon-all with the -T2pial flag cheers Bruce On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote: > > Hi FS Experts, > > The T1 and T2 images in my data set are as the attached images. Kindly do > you recommend that I do segmentation for the white matter using recon

[Freesurfer] unpacksdcmdir

Hi , The command is only used to unpack Siemens DICOM files, How can I unpack the non Siemens DICOMs? Thanks, Moahmad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informat

[Freesurfer] unpacksdcmdir

Hi , The command is only used to unpack Siemens DICOM files, How can I unpack the non Siemens DICOMs? Thanks, Moahmad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informat

Re: [Freesurfer] unpacksdcmdir

; > On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote: >> Hi , >> The command is only used to unpack Siemens DICOM files, >> How can I unpack the non Siemens DICOMs? >> >> Thanks, >> Moahmad >> ___

Re: [Freesurfer] unpacksdcmdir

...@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 3:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir did you try dcmunpack? On 10/20/2014 03:30 PM, Alshikho, Mohamad J. wrote: > Hi Doug, > But in freeSurfer wiki > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpack

Re: [Freesurfer] unpacksdcmdir

?. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Alshikho, Mohamad J. Sent: Monday, October 20, 2014 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] unpacksdcmdir Sorry I did not notice that

Re: [Freesurfer] T1 white matter segmentation

i Mohamad > > recon-all requires a T1, so use it. If the T2 is good quality you can use > it to avoid dura in a subsequent invocation of recon-all with the -T2pial > flag > > cheers > Bruce > > On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote: > >> >> Hi FS E

[Freesurfer] White matter volume

Hi Bruce, I wanted to calculate the right and left hemispheric white matter volume using a mask. Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the outputs of mris_volmmask after binarize them) and the right and left hemispheric white matter masks from aseg.mgz atlas (the outpu

Re: [Freesurfer] White matter volume

nt: Friday, October 31, 2014 10:02 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume The aseg is not surface-based and will not be as accurate doug On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote: > Hi Bruce, > I wanted to calculate the right and left h

Re: [Freesurfer] White matter volume

-volume correction that we typically compute when we estimate volumes in the stats files. cheers Bruce On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote: > Thanks Doug, > In order to improve my understanding for the analysis that I am working on > and in the process of my learning I am

Re: [Freesurfer] White matter volume

] White matter volume yes. Partial volume correction helps both accuracy and repeatability. You can certainly use our (partial-volume) corrected WM volumes and the FA from FSL if you want cheers Bruce On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote: > Hi Bruce, > Actually I am totally confused an

[Freesurfer] Tracula_average_average center

Hi Anastasia, One of Tracula's output is the "pathstats.overal.txt" and in this file we have a list of numbers. Kindly what is the difference between the metrics average and the metrics average center also which one do you recommend to do statistic? Thanks, Mohamad _

[Freesurfer] Tracula_critical issue

Hi Anastasia, I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki. The problem is that when I am repeating the third step (trac-all -path -c ) for the same subjects to generate the statistics; Tracula is updating all the informatio

[Freesurfer] White matter volume

Dear Bruce, My questions is just to learn and to improve my understanding. The commands recon-all and dt-recon are routinely generating the statistics at the end of there running and we can check the results in aseg.stats (the output of recon-all) and fa.stats (the output of dt-recon for FA). I

Re: [Freesurfer] White matter volume

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume On 11/06/2014 12:53 AM, Alshikho, Mohamad J. wrote: > > Dear Bruce, > > My questions is just to learn and to improve my understanding. > > The commands recon-all and dt-recon are routinely generating the > statistics

[Freesurfer] Critical Issue?!!

Hi Doug and Bruce, I posted this question before and I hope that you can help me to find an answer for this issue! I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki and every thing ran smoothly. The problem started when I was try

[Freesurfer] Prefrontal white matter

Hi Freesurfers, I want to calculate the FA in a VOI 8 mm3 in the left and right prefrontal white matter areas. My plan is to derive a mask for that area from aseg.mgz then I will register this mask to the FA map to calculate the FA value. Is it possible to derive like this mask from aseg.mgz and

Re: [Freesurfer] Prefrontal white matter

I would think you are better off using the wmseg for this. >> >> cheers >> Bruce >> >> >> >> >> cheers >> Bruce >> On Fri, 14 Nov >> 2014, Alshikho, Mohamad J. wrote: >> >>> Hi Freesurfers, I want to calculate the F

Re: [Freesurfer] Prefrontal white matter

; I think so, but I defer to Doug > Bruce > On Fri, 14 Nov 2014, Alshikho, Mohamad J. > wrote: > >> Doug an Bruce thanks a lot!! >> I will do the following as I understood from your orientations and kindly >> correct me if I am wrong: >> >> first of all I will

Re: [Freesurfer] Tracula_critical issue

s that you collect). You'll find that the the weighted average measures are the most reliable, as they are less affected by the tails of the distribution. a.y On Wed, 5 Nov 2014, Alshikho, Mohamad J. wrote: > Hi Anastasia, > I started recently using Tracula to do tractography for my DTI da

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