Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated?

[Tim Schäfer]

External Email - Use Caution

In your command line:

  `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507`

you run the command only for that single subject, 'subj507'. That is exactly 
what will happen, no command will be run for the other subjects, so their data 
remains unchanged. It has nothing to do with editing or not.

If you want to run again for other subjects, you would have to run the 
recon-all command with their subject IDs (one command per subject).

I hope I did not misunderstand your question?

Tim


> On January 4, 2020 at 6:09 PM Mohammad Rashid <17m...@queensu.ca> wrote:
> 
> 
> External Email - Use Caution
> 
> I recently ran this command:
> `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507` after having 
> edited aseg.mgz (there was too much matter labelled as right hippocampus, so 
> my edit was simply overwriting Right-Hippocampus voxels with 
> Right-Cerebral-White-Matter ones).
> 
> After the command's error-free completion, I checked the hippocampal volume 
> measurements of all of the participants again using asegstats2table and found 
> that they were all unchanged, except slight changes to subject subj507's 
> measurements.
> 
> So when instructed, does freesurfer only redo the reconstruction and 
> recalculate stats only for those subjects that you've edited? If so, is there 
> a way to have it recalculate every subject, not just those I've edited?
> 
> Thank you in advance.
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Question regarding T1 map from spoiled 3D GRE

[joe vanderlo]

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Thanks for the reply, Bruce! I've done some research and found the
following publication showing how T1 quantification based on the VIBE
sequence can be done offline, however, it doesn't seem to be
straightforward as hoped:
Rapid T1 quantification from high resolution 3D data with model‐based
reconstruction
10.1002/mrm.27502

Most publications I found so far use the inline map computation, which I
also tried, but got me even more inaccurate T1 values than mri_ms_fitparms
(and DESPOT1). Considering the correlation shown above, would you think it
is something that can be easily implemented?

On Sun, Jan 5, 2020 at 4:33 PM Bruce Fischl 
wrote:

> Hi Joe
>
> do you know what the forward model for VIBE is? mri_ms_fitparms uses the
> FLASH forward model of image formation then does a max likelihood
> estimation of the T1/T2*/PD using that model. If VIBE is a different model
> then it certainly won't work.
>
> cheers
> Bruce
>
>
> On Sun, 5 Jan 2020, joe vanderlo wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer community,
> >
> >
> >
> > I computed T1 maps from Siemens VIBE (a spoiled 3D GRE variant; instead
> of
> > Siemens FLASH (RF-Spoiled GRE)). I utilized mri_ms_fitparms to compute
> the
> > T1 map (which looks ok) and compared the result to a T1 map (inline) from
> > MP2RAGE.
> > However, T1 values based on Siemens VIBE (FA: 4, 8, 13, 21, 34) are much
> > lower than from MP2RAGE:
> >
> > (results from the same subject, same day/position/setup scan, same ROIs)
> >
> > WM/Corpus callosum: 652 ms (VIBE) vs 859 ms (MP2RAGE)
> > Cerebellaer WM: 583 ms vs 834 ms
> > ---
> > GM/Cortex: 845 ms vs 1184 ms
> > Deep/Inner GM: 780 ms vs 920 ms
> > ---
> > Liquor:  or 3121 vs 2758 or 3652 ms
> > Eye-Bulb: 112 vs 588
> >
> > The literature suggests (mouse brain, 3T):
> > Corpus callosum 1108±9
> > Internal capsule 913±16
> > Hippocampus 1310±15
> > Cortex 1246±28
> > (DOI: 10.1118/1.2968092)
> >
> > The literature suggests (rat brain, 3T):
> > WM: 1084 or 1110 ms
> > GM: 1820 or 1470 ms
> > (DOI: 10.1002/mrm.20605)
> >
> > However, it appears that T1 values can be quite different (Fig. 3 from
> > 10.1002/mrm.21313)
> >
> > #---#
> >
> > Therefore, I would like to ask:
> >
> > (1) Is it to be expected that T1 values differ dependent on the method
> used
> > at same field strength and same scanner/setup?
> >
> > (2) Considering that mri_ms_fitparms has not option for B1 correction,
> can I
> > "optimize" the maps in a different manner?
> > Would it make sense to run N4B on the respective VIBE scans (before map
> > computation) or maybe directly on the T1 map?
> >
> > (3) I would assume that the application of the VIBE sequence should be
> > acceptable. Are there reasons not to believe so?
> >
> > Thanks in advance
> >
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Re: [Freesurfer] Run Recon-all Parallel on Linux

[Frank Chau]

External Email - Use Caution

Dear Tim,

Sorry, I am a Linux code beginner. I installed the GNU parallel in my Linux. 
May I know how to adapt the script of “ run_reconall_parallel_wrapper.bash” to 
my own need? Thank you.

Regards

Frank

> On Jan 4, 2020, at 6:12 PM, Tim Schäfer  wrote:
> 
>External Email - Use Caution
> 
> Hi Frank,
> 
> The OS shouldn't make any difference as long as you use the same shell. You 
> will have to install GNU parallel first as it's usually not installed by 
> default under Linux (on Debian-based distros: `sudo apt-get install 
> parallel`).
> 
> I have shell scripts for the BASH shell here if you want: 
> 
>   
> https://github.com/dfsp-spirit/shell-tools/tree/master/gnu_parallel_reconall_minimal
> 
> If you need an explanation, you can read this before using them:
> 
>   
> https://www.xsmd.org/brain/2019/03/13/using-gnu-parallel-to-speedup-neuroimaging/
> 
> Best,
> 
> Tim
> 
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> 
>> On January 4, 2020 at 7:08 AM Frank Chau  wrote:
>> 
>> 
>>External Email - Use Caution
>> 
>> Dear Bruce,
>> 
>> No, I want to run recon-all on 4-8 subjects at the same time. I could find 
>> detail tutorial on the Mac platform (Run: "ls *.nii | parallel --jobs 4 
>> recon-all -s {.} -i {} -all -qcache", after installing Xcode and Homebrew.) 
>> But I couldn't find any similar information on the Linux platform.
>> 
>> Regards
>> 
>> Frank
>> 
>> On Jan 3, 2020 11:15 PM, Bruce Fischl  wrote:
>> Hi Frank
>> 
>> do you mean completing a single recon faster? The easiest way to do that
>> is to use the -openmp  flag, and set  to the number of
>> threads/cores you want to use. Alternatively if you have enough RAM you
>> can just run multiple recon-alls at the same time (which will give you a
>> bigger effective speed increase)
>> 
>> cheers
>> Bruce
>> On Fri, 3 Jan 2020, Frank Chau wrote:
>> 
>>> 
>>>External Email - Use Caution
>>> 
>>> Dear Freesurfer experts,
>>> 
>>> 
>>> May I know how to run Recon-all in parallel on Linux? I have read some
>>> source said that can use "gnu parallel" to complete it. But they do not
>>> describe it in detail how to perform it.
>>> 
>>> 
>>> Regards
>>> 
>>> 
>>> Frank
>>> 
>>> ---
>>> 
>>> FRANK  C Y CHAU
>>> 
>>> 
>>> Research assistant
>>> 
>>> Division of Neurology
>>> 
>>> Department of Medicine
>>> 
>>> 
>>> Tel: +852 6340 2553
>>> 
>>> Fax: 2872 5828
>>> 
>>> 
>>> E-mail : cyfr...@hku.hk
>>> 
>>> 
>>> 
>>> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road,
>>> Hong Kong
>>> 
>>> 
>>> 
>> 
>> ___
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> 
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Re: [Freesurfer] Run Recon-all Parallel on Linux

[Tim Schäfer]

External Email - Use Caution

Dear Frank,

I have updated the header of the script with much more detailed instructions. I 
hope they help. If not, let me know where you are stuck.

Tim

> On January 6, 2020 at 2:56 PM Frank Chau  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear Tim,
> 
> Sorry, I am a Linux code beginner. I installed the GNU parallel in my Linux. 
> May I know how to adapt the script of “ run_reconall_parallel_wrapper.bash” 
> to my own need? Thank you.
> 
> Regards
> 
> Frank
> 
> > On Jan 4, 2020, at 6:12 PM, Tim Schäfer  wrote:
> > 
> >External Email - Use Caution
> > 
> > Hi Frank,
> > 
> > The OS shouldn't make any difference as long as you use the same shell. You 
> > will have to install GNU parallel first as it's usually not installed by 
> > default under Linux (on Debian-based distros: `sudo apt-get install 
> > parallel`).
> > 
> > I have shell scripts for the BASH shell here if you want: 
> > 
> >   
> > https://github.com/dfsp-spirit/shell-tools/tree/master/gnu_parallel_reconall_minimal
> > 
> > If you need an explanation, you can read this before using them:
> > 
> >   
> > https://www.xsmd.org/brain/2019/03/13/using-gnu-parallel-to-speedup-neuroimaging/
> > 
> > Best,
> > 
> > Tim
> > 
> > --
> > Dr. Tim Schäfer
> > Postdoc Computational Neuroimaging
> > Department of Child and Adolescent Psychiatry, Psychosomatics and 
> > Psychotherapy
> > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> > 
> >> On January 4, 2020 at 7:08 AM Frank Chau  wrote:
> >> 
> >> 
> >>External Email - Use Caution
> >> 
> >> Dear Bruce,
> >> 
> >> No, I want to run recon-all on 4-8 subjects at the same time. I could find 
> >> detail tutorial on the Mac platform (Run: "ls *.nii | parallel --jobs 4 
> >> recon-all -s {.} -i {} -all -qcache", after installing Xcode and 
> >> Homebrew.) But I couldn't find any similar information on the Linux 
> >> platform.
> >> 
> >> Regards
> >> 
> >> Frank
> >> 
> >> On Jan 3, 2020 11:15 PM, Bruce Fischl  wrote:
> >> Hi Frank
> >> 
> >> do you mean completing a single recon faster? The easiest way to do that
> >> is to use the -openmp  flag, and set  to the number of
> >> threads/cores you want to use. Alternatively if you have enough RAM you
> >> can just run multiple recon-alls at the same time (which will give you a
> >> bigger effective speed increase)
> >> 
> >> cheers
> >> Bruce
> >> On Fri, 3 Jan 2020, Frank Chau wrote:
> >> 
> >>> 
> >>>External Email - Use Caution
> >>> 
> >>> Dear Freesurfer experts,
> >>> 
> >>> 
> >>> May I know how to run Recon-all in parallel on Linux? I have read some
> >>> source said that can use "gnu parallel" to complete it. But they do not
> >>> describe it in detail how to perform it.
> >>> 
> >>> 
> >>> Regards
> >>> 
> >>> 
> >>> Frank
> >>> 
> >>> ---
> >>> 
> >>> FRANK  C Y CHAU
> >>> 
> >>> 
> >>> Research assistant
> >>> 
> >>> Division of Neurology
> >>> 
> >>> Department of Medicine
> >>> 
> >>> 
> >>> Tel: +852 6340 2553
> >>> 
> >>> Fax: 2872 5828
> >>> 
> >>> 
> >>> E-mail : cyfr...@hku.hk
> >>> 
> >>> 
> >>> 
> >>> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam 
> >>> Road,
> >>> Hong Kong
> >>> 
> >>> 
> >>> 
> >> 
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > ___
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> 
> 
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Unable to run recon all

[Greve, Douglas N.,Ph.D.]

It is not clear why it failed for these subjects (always happens at the 
same place). Can you upload one of them for me to take a look at? here 
are the instructions

 From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.



On 1/6/20 11:49 AM, Sahil Bajaj wrote:
>
> External Email - Use Caution
>
> Hi Dough,
>
> I finished recon -all on about 515 subjects and I get error in 11 out 
> of 515 subjects. Here I am attaching recon-all.log files of all those 
> 11 subjects. I would really appreciate your help in fixing these errors.
>
> Thanks,
> Sahil
>
> On Thu, Jan 2, 2020 at 10:03 AM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Can you send the recon-all.log file? You sent the .error file
>
> On 12/20/2019 10:13 AM, Sahil Bajaj wrote:
>>
>> External Email - Use Caution
>>
>> Hello FS experts,
>>
>> I am trying to run recon all on about 100 subjects. But one out
>> of 100 subjects finishes recon all with error, and doesn't
>> complete the process. Here I am attaching recon all log for your
>> reference. Also, before installing freesurfer on MAC Catalina, I
>> ran sudo spctl - -master -disable
>>
>> I would really appreciate any help in resolving this.
>>
>> Thanks,
>> Sahil
>> 1) FreeSurfer version:
>>
>> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>>
>> 2) Platform: MACOS Catalina
>> 3) recon-all.log: see attached
>>
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>
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Re: [Freesurfer] Cortical inflation and maintenance of surface voxel intensity

[Greve, Douglas N.,Ph.D.]

Hi Pedro, what you are trying to do is certainly possible. It looks like 
you are doing the right thing as far as I can tell, but I got a little 
lost after step 4, particularly the "Analyze measured signal" step. One 
other thing that may be an issue is what projection fraction you used in 
the mri_vol2surf step.

On 12/30/19 2:21 PM, Assis Lopes, Pedro Augusto wrote:
>
> Dear Freesurfer experts,
>
> I am a medical student and am currently doing a fellowship at the JPK 
> Stroke Research Center - MGH. My current research project involves 
> measuring the area of a cortical hypointense brain MRI signal 
> (cortical superficial siderosis) , a marker that lays along the 
> subarachnoid space/pial surface, only visible in blood sensitive MRI 
> (SWI in my case).
>
> In summary:
>
> We are trying to do a parallel to fMRI studies (fMRI x T1w // SWI x 
> T1w), analyzing SWI signal intensity on a registered inflated brain 
> surface;
>
> Projecting SWI surface intensity would then allow manual area 
> demarcation of hipointensities in a flat surface.
>
> Here is our step-by-step plan (analogous to fMRIxT1w registration/BOLD 
> signal intensity projection to surface):
>
>  1. Perform freesurfer recon-all of the subject in question to
> generate subject-surface models.
>  2. BET and register the image of interest (SWI) into the
> freesurfer-subject space (register both SWI and MEMPRAGE
> sequences) [bbregister]
>  3. Having SWI in subject space and a surface model (generated in 1);
>  1. Split registered SWI into LH and RH
>  2. Tkregister2 to get LTA to mri_vol2surf format
>  3. Mri_vol2surf each hemisphere to the recon output
>  4. Display the SWI hemi surface as an overlay
>  5. Inflate T1 surface and observe its SWI overlay;
>  1. Manual demarcation of characteristic SWI hypointense signals
>  6. Analyze measured signal
>
> _We did try this approach_, but yet with these steps we could only 
> obtain an inflated cortical surface representation that has _no 
> correspondence to SWI`s intensity_.
>
> So, here comes the question:
>
> *If BOLD signal intensity can be projected onto surface area; is there 
> a way to project SWI intensity onto the cortical surface?*
>
> Or
>
> Can we preserve the info of SWI surface voxel intensity while doing 
> the surface inflation?
>
> If not
>
> Is it possible to use the positional information of t1w voxel (used in 
> inflation process) as an index to retrieve its correspondent SWI 
> intensity value?
>
> Sorry for the long question. In advance I thank you already for being 
> so attentive.
>
> Best,
>
> Pedro
>
> Pedro Augusto Assis Lopes
>
> Student Researcher
> J. Philip Kistler Stroke Research Center
> Massachusetts General Hospital
> 175 Cambridge Street, Suite 300
> Boston, MA  02114
>
> Phone: (617) 643-3940
>
>
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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

This is not making any sense to me. Are you sure you are in 
$SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that 
BN_Atlas_subcotex.mgz is in the same folder?

On 1/3/20 3:07 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Thank you for testing it. As before I get the same error message.
> Do you know what I´m doing wrong here?
>
> Best,
> Boris
>
> MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
> subject 1122
> outvol aparc+BN_Atlas_subcotex.mgz
> useribbon 0
> baseoffset 0
> RipUnknown 0
>
> Reading lh white surface
>  /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
>
> Reading lh pial surface
>  /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
>
> Loading lh annotations from 
> /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>
> Reading rh white surface
>  /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
>
> Reading rh pial surface
>  /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
>
> Loading rh annotations from 
> /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> Have color table for lh white annotation
> Have color table for rh white annotation
> Loading ribbon segmentation from 
> /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
> ERROR: cannot find aseg
> MacBook-Pro:mri boris$
>
>
>> Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>>:
>>
>> OK, using the data you sent I was able to get mri_aparc2aseg to run. 
>> Can you try this command again?
>>
>> On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
>>>
>>> External Email - Use Caution
>>>
>>> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
>>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
>>> SUBJECTS_DIR /Users/boris/Desktop/mydir
>>> subject 1122
>>> outvol aparc+BN_Atlas_subcotex.mgz
>>> useribbon 0
>>> baseoffset 0
>>> RipUnknown 0
>>>
>>> Reading lh white surface
>>>  /Users/boris/Desktop/mydir/1122/surf/lh.white
>>>
>>> Reading lh pial surface
>>>  /Users/boris/Desktop/mydir/1122/surf/lh.pial
>>>
>>> Loading lh annotations from 
>>> /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
>>> reading colortable from annotation file...
>>> colortable with 36 entries read (originally 
>>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>>>
>>> Reading rh white surface
>>>  /Users/boris/Desktop/mydir/1122/surf/rh.white
>>>
>>> Reading rh pial surface
>>>  /Users/boris/Desktop/mydir/1122/surf/rh.pial
>>>
>>> Loading rh annotations from 
>>> /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
>>> reading colortable from annotation file...
>>> colortable with 36 entries read (originally 
>>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>>> Have color table for lh white annotation
>>> Have color table for rh white annotation
>>> Loading ribbon segmentation from 
>>> /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
>>>
>>> Building hash of lh white
>>>
>>> Building hash of lh pial
>>>
>>> Building hash of rh white
>>>
>>> Building hash of rh pial
>>> ERROR: cannot find aseg
>>>
>>>
>>> I get the same result using aseg.mgz
>>>
>>> Thanks,
>>> Boris
 Am 12.12.2019 um 17:37 schrieb Bruce Fischl 
 mailto:fis...@nmr.mgh.harvard.edu>>:

 Hi Boris

 can you send us the full command line and screen output of the 
 commands that are failing?

 cheers
 Bruce
 On Thu, 12 Dec 2019, Boris Rauchmann wrote:

> External Email - Use Caution
> Thanks. unfortunately I get an error message when I use the --aseg 
> flag for BN_Atlas_subcotex.mgz but
> even, if I'm using the original aseg.mgz I get: ERROR: cannot find 
> aseg
> .../fs_all_subjects/xyz/mri/aseg.mgz
> The file BN_Atlas_subcotex.mgz was created using:
> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
> Best,
> Boris
> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but 
> with your
>  subcortical ROIs added? If so, you can try merging it with 
> the aparc, eg,
>
>  mri_aparc2aseg --s subject --

Re: [Freesurfer] Unable to run recon all

[Sahil Bajaj]

External Email - Use Caution

Hi Dough,

I just uploaded one of the files on Martinos Center File Drop
. I hope that works !
(Somehow, uploading through ftp was taking too long).

Thanks.

On Mon, Jan 6, 2020 at 11:19 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> It is not clear why it failed for these subjects (always happens at the
> same place). Can you upload one of them for me to take a look at? here
> are the instructions
>
>  From the linux command line,
> Create the file you want to upload, eg,
> cd $SUBJECTS_DIR
> tar cvfz subject.tar.gz ./subject
> Now log  into our anonymous FTP site:
> ftp surfer.nmr.mgh.harvard.edu
> It will ask you for a user name: use "anonymous" (no quotes)
> It will ask you for a password: use "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
>
>
>
> On 1/6/20 11:49 AM, Sahil Bajaj wrote:
> >
> > External Email - Use Caution
> >
> > Hi Dough,
> >
> > I finished recon -all on about 515 subjects and I get error in 11 out
> > of 515 subjects. Here I am attaching recon-all.log files of all those
> > 11 subjects. I would really appreciate your help in fixing these errors.
> >
> > Thanks,
> > Sahil
> >
> > On Thu, Jan 2, 2020 at 10:03 AM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Can you send the recon-all.log file? You sent the .error file
> >
> > On 12/20/2019 10:13 AM, Sahil Bajaj wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Hello FS experts,
> >>
> >> I am trying to run recon all on about 100 subjects. But one out
> >> of 100 subjects finishes recon all with error, and doesn't
> >> complete the process. Here I am attaching recon all log for your
> >> reference. Also, before installing freesurfer on MAC Catalina, I
> >> ran sudo spctl - -master -disable
> >>
> >> I would really appreciate any help in resolving this.
> >>
> >> Thanks,
> >> Sahil
> >> 1) FreeSurfer version:
> >>
> >> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >>
> >> 2) Platform: MACOS Catalina
> >> 3) recon-all.log: see attached
> >>
> >> ___
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> >
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> >
>
>
>
> 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
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[Freesurfer] Recommendation for CFT and CWT FreeSurfer analysis

[Martin Juneja]

External Email - Use Caution

Hi,

I am using Monte-Carlo simulations (for cortical thickness and volume -
behavioral analysis) for clusterwise correction for multiple comparisons.

My results are either significant at (i) CFT < 0.001 and CWT < 0.1 (i.e.,
CWT = 0.07) (smoothing 12 mm) for cortical thickness-behavior analysis -
with maxima at -4.3 (CFT)
or (ii) CFT < 0.05 and CWT < 0.001 (i.e., CWT = 0.0002) (smoothing 10 mm)
for cortical volume-behavior - with maxima at -4.53 (CFT)

Both the clusters in (i) (lateral orbital frontal) and (ii) (rostral
middle) are within the frontal cortex, but not overlapping !
Also, although maxima is at (i) -4.3 and (ii) -4.53, still the clusters do
not survive recommended thresholds suggested in
https://www.ncbi.nlm.nih.gov/pubmed/29288131
And the FPR in this paper at strong CWT (i..e, 0.001) and liberal CFT
(i..e, 0.05) is not calculated.

So I was wondering if there is any recommendation from the experts
regarding these results, or none of these make sense because I never get
CFT < 0.001 and CWT < 0.05 (at-least).

Any help would be really appreciated.
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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

I’m sure just double checked it. I don’t know what’s wrong here. 

Von meinem iPhone gesendet

>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. 
>> :
> This is not making any sense to me. Are you sure you are in 
> $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that 
> BN_Atlas_subcotex.mgz is in the same folder?
> 
>> On 1/3/20 3:07 PM, Boris Rauchmann wrote:
>> 
>> External Email - Use Caution
>> 
>> Thank you for testing it. As before I get the same error message.
>> Do you know what I´m doing wrong here?
>> 
>> Best,
>> Boris
>> 
>> MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
>> SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
>> subject 1122
>> outvol aparc+BN_Atlas_subcotex.mgz
>> useribbon 0
>> baseoffset 0
>> RipUnknown 0
>> 
>> Reading lh white surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
>> 
>> Reading lh pial surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
>> 
>> Loading lh annotations from 
>> /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally 
>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>> 
>> Reading rh white surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
>> 
>> Reading rh pial surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
>> 
>> Loading rh annotations from 
>> /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally 
>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>> Have color table for lh white annotation
>> Have color table for rh white annotation
>> Loading ribbon segmentation from 
>> /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
>> 
>> Building hash of lh white
>> 
>> Building hash of lh pial
>> 
>> Building hash of rh white
>> 
>> Building hash of rh pial
>> ERROR: cannot find aseg
>> MacBook-Pro:mri boris$
>> 
>> 
>>> Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D.
>>> mailto:dgr...@mgh.harvard.edu>>:
>>> OK, using the data you sent I was able to get mri_aparc2aseg to run.
>>> Can you try this command again?
>>> On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
 External Email - Use Caution
 My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
 BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
 SUBJECTS_DIR /Users/boris/Desktop/mydir
 subject 1122
 outvol aparc+BN_Atlas_subcotex.mgz
 useribbon 0
 baseoffset 0
 RipUnknown 0
 Reading lh white surface
  /Users/boris/Desktop/mydir/1122/surf/lh.white
 Reading lh pial surface
  /Users/boris/Desktop/mydir/1122/surf/lh.pial
 Loading lh annotations from
 /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
 reading colortable from annotation file...
 colortable with 36 entries read (originally
 /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
 Reading rh white surface
  /Users/boris/Desktop/mydir/1122/surf/rh.white
 Reading rh pial surface
  /Users/boris/Desktop/mydir/1122/surf/rh.pial
 Loading rh annotations from
 /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
 reading colortable from annotation file...
 colortable with 36 entries read (originally
 /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
 Have color table for lh white annotation
 Have color table for rh white annotation
 Loading ribbon segmentation from
 /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
 Building hash of lh white
 Building hash of lh pial
 Building hash of rh white
 Building hash of rh pial
 ERROR: cannot find aseg
 I get the same result using aseg.mgz
 Thanks,
 Boris
> Am 12.12.2019 um 17:37 schrieb Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>>:
> Hi Boris
> can you send us the full command line and screen output of the
> commands that are failing?
> cheers
> Bruce
> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
>> External Email - Use Caution
>> Thanks. unfortunately I get an error message when I use the --aseg
>> flag for BN_Atlas_subcotex.mgz but
>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find
>> aseg
>> .../fs_all_subjects/xyz/mri/aseg.mgz
>> The file BN_Atlas_subcotex.mgz was created using:
>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
>> Best,
>> Boris
>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D.
>> mailto

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

Are you sure you have permission to view that file?

On 1/6/20 5:01 PM, Boris Rauchmann wrote:
>  External Email - Use Caution
>
> I’m sure just double checked it. I don’t know what’s wrong here.
>
> Von meinem iPhone gesendet
>
>>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. 
>>> :
>> This is not making any sense to me. Are you sure you are in
>> $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that
>> BN_Atlas_subcotex.mgz is in the same folder?
>>
>>> On 1/3/20 3:07 PM, Boris Rauchmann wrote:
>>>
>>>  External Email - Use Caution
>>>
>>> Thank you for testing it. As before I get the same error message.
>>> Do you know what I´m doing wrong here?
>>>
>>> Best,
>>> Boris
>>>
>>> MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg
>>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
>>> SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
>>> subject 1122
>>> outvol aparc+BN_Atlas_subcotex.mgz
>>> useribbon 0
>>> baseoffset 0
>>> RipUnknown 0
>>>
>>> Reading lh white surface
>>>   /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
>>>
>>> Reading lh pial surface
>>>   /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
>>>
>>> Loading lh annotations from
>>> /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot
>>> reading colortable from annotation file...
>>> colortable with 36 entries read (originally
>>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>>>
>>> Reading rh white surface
>>>   /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
>>>
>>> Reading rh pial surface
>>>   /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
>>>
>>> Loading rh annotations from
>>> /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot
>>> reading colortable from annotation file...
>>> colortable with 36 entries read (originally
>>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>>> Have color table for lh white annotation
>>> Have color table for rh white annotation
>>> Loading ribbon segmentation from
>>> /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
>>>
>>> Building hash of lh white
>>>
>>> Building hash of lh pial
>>>
>>> Building hash of rh white
>>>
>>> Building hash of rh pial
>>> ERROR: cannot find aseg
>>> MacBook-Pro:mri boris$
>>>
>>>
 Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D.
 mailto:dgr...@mgh.harvard.edu>>:
 OK, using the data you sent I was able to get mri_aparc2aseg to run.
 Can you try this command again?
 On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
>  External Email - Use Caution
> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> SUBJECTS_DIR /Users/boris/Desktop/mydir
> subject 1122
> outvol aparc+BN_Atlas_subcotex.mgz
> useribbon 0
> baseoffset 0
> RipUnknown 0
> Reading lh white surface
>   /Users/boris/Desktop/mydir/1122/surf/lh.white
> Reading lh pial surface
>   /Users/boris/Desktop/mydir/1122/surf/lh.pial
> Loading lh annotations from
> /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> Reading rh white surface
>   /Users/boris/Desktop/mydir/1122/surf/rh.white
> Reading rh pial surface
>   /Users/boris/Desktop/mydir/1122/surf/rh.pial
> Loading rh annotations from
> /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> Have color table for lh white annotation
> Have color table for rh white annotation
> Loading ribbon segmentation from
> /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
> Building hash of lh white
> Building hash of lh pial
> Building hash of rh white
> Building hash of rh pial
> ERROR: cannot find aseg
> I get the same result using aseg.mgz
> Thanks,
> Boris
>> Am 12.12.2019 um 17:37 schrieb Bruce Fischl
>> mailto:fis...@nmr.mgh.harvard.edu>>:
>> Hi Boris
>> can you send us the full command line and screen output of the
>> commands that are failing?
>> cheers
>> Bruce
>> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
>>>  External Email - Use Caution
>>> Thanks. unfortunately I get an error message when I use the --aseg
>>> flag for BN_Atlas_subcotex.mgz but
>>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find
>>> aseg
>>> .../fs_all_subjects/xyz/mri/aseg.mgz
>>> The file BN_Atlas_subcotex.mgz was created using:
>>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
>>> $SUBJECTS_DIR/xyz/mri/transforms/talai

Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated?

[Mohammad Rashid]

External Email - Use Caution

Ah okay, I understand now, thank you very much for the help! In hindsight this 
was a stupid question. What you said makes things perfectly clear. Thanks again!

From: Mohammad Rashid <17m...@queensu.ca>
Sent: Monday, January 6, 2020 12:04 PM
To: Tim Schäfer 
Subject: Re: [Freesurfer] When rerunning recon-all from a later stage, are only 
edited participants' reconstructions recalculated?

Ah okay, I understand now, thank you very much for the help! In hindsight this 
was a stupid question. What you said makes things perfectly clear. Thanks again!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tim Schäfer 

Sent: Monday, January 6, 2020 3:29 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] When rerunning recon-all from a later stage, are only 
edited participants' reconstructions recalculated?

External Email - Use Caution

In your command line:

  `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507`

you run the command only for that single subject, 'subj507'. That is exactly 
what will happen, no command will be run for the other subjects, so their data 
remains unchanged. It has nothing to do with editing or not.

If you want to run again for other subjects, you would have to run the 
recon-all command with their subject IDs (one command per subject).

I hope I did not misunderstand your question?

Tim


> On January 4, 2020 at 6:09 PM Mohammad Rashid <17m...@queensu.ca> wrote:
>
>
> External Email - Use Caution
>
> I recently ran this command:
> `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507` after having 
> edited aseg.mgz (there was too much matter labelled as right hippocampus, so 
> my edit was simply overwriting Right-Hippocampus voxels with 
> Right-Cerebral-White-Matter ones).
>
> After the command's error-free completion, I checked the hippocampal volume 
> measurements of all of the participants again using asegstats2table and found 
> that they were all unchanged, except slight changes to subject subj507's 
> measurements.
>
> So when instructed, does freesurfer only redo the reconstruction and 
> recalculate stats only for those subjects that you've edited? If so, is there 
> a way to have it recalculate every subject, not just those I've edited?
>
> Thank you in advance.
> ___
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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[Freesurfer] Freesurfer 7T MPRAGE

[Manoj Saranathan]

External Email - Use Caution

Hi,


I am trying to process 7T MPRAGE data (not MP2RAGE) using recon-all. In 
previous threads, a few people have suggested using SPM to correct for bias 
first and then running recon-all. Alternatively I saw a thread which suggests 
modifying the mri_nu_correct command

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61913.html



Can I edit the recon-all to run this alternative command and simply run 
recon-all?  The threads are all really old and SPM is now SPM12 which 
integrates things. Is this modified bias correction inside FS as good as SPM ? 
I am mainly interested in thalamic segmentation.


Are there others with the same issue?


Thanks


manoj


Manoj Saranathan
Associate Professor, Dept. of Medical Imaging
University of Arizona
Ph: 520-626-6531

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[Freesurfer] pcc.mgh files from mri_glmfit using --pvr

[Emilie Reas]

External Email - Use Caution

I am running mri_glmfit using the --pvr option and do not get a pcc.mgh
file with the output. I found an old thread from 2017 in which Douglas
Greve explained that "mri_glmfit will not generate a pcc file with --pvr. I
think I just did not get around to adding support for this."

Have there been any updates to fix this? Is there a workaround to get pcc
files using --pvr?
-- 
Emilie Reas, PhD
Postdoctoral Fellow, UC San Diego
er...@ucsd.edu
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Re: [Freesurfer] Cortical inflation and maintenance of surface voxel intensity

[Assis Lopes, Pedro Augusto]

Dear Freesurfer experts,

Thank you for the quick response Dr. Greve! It`s an attempt to measure 
siderosis area, a thin (pathologically), small and blooming cortical signal 
seen through SWI (due to B0 inhomogeneity). We did:
Recon-all 

SWI BET and registration to T1
#BET
bet $SUBJECTS_DIR/$subject/SWI_Surface/original/$subject\_SWI.nii.gz 
$SUBJECTS_DIR/$subject/SWI_Surface/bet/$subject\_SWI-bet.nii.gz -R 

#bbregister (SWI to T1 skull stripped output from recon all)
bbregister --s $subject --mov 
$SUBJECTS_DIR/$subject/SWI_Surface/bet/$subject\_SWI-bet.nii.gz --reg 
$SUBJECTS_DIR/$subject/SWI_Surface/bbreg/$subject\_SWI_bbreg.dat --o 
$SUBJECTS_DIR/$subject/SWI_Surface/bbreg/$subject\_SWI_bbreg.nii.gz --t1   

#Divided hemispheres 
#LH and RH
mri_binarize --i 
$SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_filled.nii.gz --match 255 --o 
$SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_filled_LH.nii.gz
mri_mask $SUBJECTS_DIR/$subject/SWI_Surface/bbreg/$subject\_SWI_bbreg.nii.gz 
$SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_filled_LH.nii.gz 
$SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_SWI-LH.nii.gz

#Transform the volume into a surface file with mri_vol2surf 
#Left Hemi
mri_vol2surf --mov 
$SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_SWI-LH.nii.gz --srcreg 
$SUBJECTS_DIR/$subject/SWI_Surface/bbreg/$subject\_SWI_bbreg.lta --hemi lh --o 
$SUBJECTS_DIR/$subject/SWI_Surface/vol2surf/$subject\_SWI-LH_surface.nii.gz 
--regheader $subject
#and right 
mri_vol2surf --mov 
$SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_SWI-RH.nii.gz --srcreg 
$SUBJECTS_DIR/$subject/SWI_Surface/bbreg/$subject\_SWI_bbreg.lta --hemi rh --o 
$SUBJECTS_DIR/$subject/SWI_Surface/vol2surf/$subject\_SWI-RH_surface.nii.gz 
--regheader $subject

#Freeview and project SWI as an overlay onto the inflated surface
freeview -f 
$SUBJECTS_DIR/$subject/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=$SUBJECTS_DIR/$subject/SWI_Surface/vol2surf/$subject\_SWI-LH_surface.nii.gz
 -f 
$SUBJECTS_DIR/$subject/surf/rh.inflated:annot=aparc.annot:annot_outline=1:overlay=$SUBJECTS_DIR/$subject/SWI_Surface/vol2surf/$subject\_SWI-RH_surface.nii.gz

We did not specify any projection fraction in our mri_vol2surf. Sorry for not 
being clearer in the step of analyze measured signal. We aim to make a brain 
mask of such hypointense signal and obtain its proportional area to total brain 
pial surface.

 Thank you so much for the attention Dr. Greve, I look forward in receiving 
your response!


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Greve, Douglas N.,Ph.D.
Sent: Monday, January 06, 2020 12:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Cortical inflation and maintenance of surface voxel 
intensity

Hi Pedro, what you are trying to do is certainly possible. It looks like you 
are doing the right thing as far as I can tell, but I got a little lost after 
step 4, particularly the "Analyze measured signal" step. One other thing that 
may be an issue is what projection fraction you used in the mri_vol2surf step.

On 12/30/19 2:21 PM, Assis Lopes, Pedro Augusto wrote:
>
> Dear Freesurfer experts,
>
> I am a medical student and am currently doing a fellowship at the JPK 
> Stroke Research Center - MGH. My current research project involves 
> measuring the area of a cortical hypointense brain MRI signal 
> (cortical superficial siderosis) , a marker that lays along the 
> subarachnoid space/pial surface, only visible in blood sensitive MRI 
> (SWI in my case).
>
> In summary:
>
> We are trying to do a parallel to fMRI studies (fMRI x T1w // SWI x 
> T1w), analyzing SWI signal intensity on a registered inflated brain 
> surface;
>
> Projecting SWI surface intensity would then allow manual area 
> demarcation of hipointensities in a flat surface.
>
> Here is our step-by-step plan (analogous to fMRIxT1w registration/BOLD 
> signal intensity projection to surface):
>
>  1. Perform freesurfer recon-all of the subject in question to
> generate subject-surface models.
>  2. BET and register the image of interest (SWI) into the
> freesurfer-subject space (register both SWI and MEMPRAGE
> sequences) [bbregister]
>  3. Having SWI in subject space and a surface model (generated in 1);
>  1. Split registered SWI into LH and RH
>  2. Tkregister2 to get LTA to mri_vol2surf format
>  3. Mri_vol2surf each hemisphere to the recon output  4. Display 
> the SWI hemi surface as an overlay  5. Inflate T1 surface and observe 
> its SWI overlay;
>  1. Manual demarcation of characteristic SWI hypointense signals  
> 6. Analyze measured signal
>
> _We did try this approach_, but yet with these steps we could only 
> obtain an inflated cortical surface representation that has _no 
> correspondence to SWI`s intensity_.
>
> So, here comes the question:
>
> *If BOLD signal intensity can be projected onto surface area; is 

Re: [Freesurfer] Freesurfer 7T MPRAGE

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

Dear Manoj,


in case you want to rely on tools provided with FreeSurfer only, N3 can produce 
good results even for 7T data. However, in my experience, you need to supply a 
brainmask to N3 to achieve very similar results compared to SPM. Otherwise, 
especially around the temporal lobes the inhomogeneity will not be corrected 
sufficiently.


Tweaking recon-all for this is possible, but is slightly more complicated than 
changing the parameters of mri_nu_correct only. Furthermore, the procedure may 
change in case you use higher resolution 7T data.


Apart from that SPM, N3 as well as N4 of ANTs (also using a brainmask) will all 
produce similar results. I mostly use SPM for pre-processing my 7T data as it 
is the easiest to use in my processing pipeline.


Best,

Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Manoj Saranathan 

Gesendet: Montag, 6. Januar 2020 23:51:23
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Freesurfer 7T MPRAGE


External Email - Use Caution

Hi,


I am trying to process 7T MPRAGE data (not MP2RAGE) using recon-all. In 
previous threads, a few people have suggested using SPM to correct for bias 
first and then running recon-all. Alternatively I saw a thread which suggests 
modifying the mri_nu_correct command

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61913.html



Can I edit the recon-all to run this alternative command and simply run 
recon-all?  The threads are all really old and SPM is now SPM12 which 
integrates things. Is this modified bias correction inside FS as good as SPM ? 
I am mainly interested in thalamic segmentation.


Are there others with the same issue?


Thanks


manoj


Manoj Saranathan
Associate Professor, Dept. of Medical Imaging
University of Arizona
Ph: 520-626-6531



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