[Freesurfer] Could not login in "https://mail.nmr.mgh.harvard.edu/NMRAuth/GLOBAL/LOGIN"

[ZhangBo]

External Email - Use Caution

Hi teams,
I could not login in "Could not login in 
"https://mail.nmr.mgh.harvard.edu/NMRAuth/GLOBAL/LOGIN";. Thanks.

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[Freesurfer] aparc a2009s stats ROI names don't match ColorLUT for FS 6.0

[Don Hagler]

External Email - Use Caution

I have recently started using FreeSurfer 6.0 after previously working with 5.3 
for several years. I found that the lh.aparc.a2009s.stats files use different 
ROI names (e.g., G_frontomargin) than they did in FS5.3 
(G_and_S_frontomargin). However, the FreeSurferColorLUT.txt file still has the 
old names.

What caused the ROI names to change for the a2009s.stats files? Was the 
ColorLUT supposed to have been updated but wasn’t? Where do those shorter names 
come from? Is there already a mapping file for the different versions of the 
names?

Because some of the parcel names in the stats files no longer match the LUT, my 
existing code for compiling FreeSurfer results fails to load the results for 
those ROIs with new names.

I think I can find a work-around for this, such as using a mapping file or a 
renaming rule applied to the a2009s stats ROI names, before matching to the LUT.

But I thought I would email this list to raise the issue. I searched the 
archives and didn’t see something similar, so maybe no one else tries to match 
those names to the LUT.

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Re: [Freesurfer] Tracula Inquiry

[Paul Wighton]

External Email - Use Caution

Hi Jason,

Tracula depends on FSL.  If you have FSL installed, all that should be
needed is to define FSL_DIR before sourcing
`$FREESURFER_HOME/SetUpFreeSurfer.sh`

So using your example above, you could go

```
export FREESURFER_HOME=/Applications/freesurfer
export FSL_DIR=/location/of/fsl/binaries
source $FREESURFER_HOME/SetUpFreeSurfer.sh
```

-Paul


On Thu, Mar 5, 2020 at 12:45 PM Ledesma, Jason 
wrote:

> External Email - Use Caution
>
> Hello,
>
>
> I am having trouble carrying out Tracula on Freesurfer. See the following
> script (for confidentiality, patient's name has been replaced by XXX):
>
>
> Admins-iMac:~ neurology$ export FREESURFER_HOME=/Applications/freesurfer
>
> Admins-iMac:~ neurology$
>
> Admins-iMac:~ neurology$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
>  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>
> FREESURFER_HOME   /Applications/freesurfer
>
> FSFAST_HOME   /Applications/freesurfer/fsfast
>
> FSF_OUTPUT_FORMAT nii.gz
>
> SUBJECTS_DIR  /Applications/freesurfer/subjects
>
> MNI_DIR   /Applications/freesurfer/mni
>
> Admins-iMac:~ neurology$ export
> SUBJECTS_DIR=/Applications/freesurfer/subjects/XXX
>
> Admins-iMac:~ neurology$ cd /Applications/freesurfer/subjects/XXX
>
> Admins-iMac:XXX neurology$ trac-all -prep -c XXX7.24.14Configfile
>
> FSLDIR: Undefined variable.
>
> Admins-iMac:XXX neurology$
>
> My Config text file has the following info:
>
>
> setenv SUBJECTS_DIR Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri
>
> set dtroot = Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri
>
> set subjlist = (XXX7.24.14)
>
> set dcmroot = Applications/freesurfer/subjects/XXX/XXX7.24.14AXDWI
>
> set dcmlist = ( MR0001.dcm )
>
> set bvecfile =
> (Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bvec.txt)
>
> set bvalfile =
> (Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bval.txt)
>
> set doeddy = 1
>
> set dorotbvecs = 1
>
> set usemaskanat = 1
>
> set threat = 0.3
>
> set doregflt = 0
>
> set doregbbr = 1
>
> set doregmni = 1
>
> set doregcvs = 0
>
> set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
>
> set pathlist = ( lh.cst_AS rh.cst_AS \
>
>lh.ilf_AS rh.ilf_AS \
>
>lh.unc_AS rh.unc_AS \
>
>fmajor_PP fminor_PP \
>
>lh.atr_PP rh.atr_PP \
>
>lh.cab_PP rh.cab_PP \
>
>lh.ccg_PP rh.ccg_PP \
>
>lh.slfp_PP rh.slfp_PP \
>
>lh.slft_PP rh.slft_PP )
>
> set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
>
> Please advise. Thanks.
>
>
> Sincerely,
>
> Jason Ledesma
> Staff Research Associate
> Phone: 1(424)571-7755
> E-mail: jason.lede...@labiomed.org
>
>
>
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[Freesurfer] PetSurfer reference region

[Dincer, Aylin]

External Email - Use Caution

Hello PetSurfer experts,

We are using the cerebellum cortex as our reference region, but noticed that 
the SUVR values for lh/rh cerebellum cortex do not have a value of 1 (which is 
what we were expecting). The actual SUVR values are 1.31 for the lh and 1.35 
for the rh cerebellum cortex. I attached the stats file (gtm.stats.dat) and 
below is the command we ran.

mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf ${FWHM} 
--seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF+2 .01 --mgx 
.01 --rescale 8 47 -o regmean_gtmpvc_output

Let me know if you need any more details.

Thanks so much,
Aylin



_
Aylin Dincer
Senior Research Technician
NeuroImaging Laboratories
Imaging Core, Benzinger Lab
314-362-3629



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gtm.stats.dat
Description: gtm.stats.dat
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Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

[Frank Chau]

External Email - Use Caution

Dear Tim,

Is it the FOV of my T1 image will affect the process Recon-all? If yes, how 
would it impact my output results?

Regards

Frank


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

Sent: 05 March 2020 2:25
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution

Thanks for providing the image. Looks fine to me as well.

What is a bit strange is that when running `mri_info` on the file you provided, 
it shows a FOV of 256 (not 284!) for me, so I have no idea why this error is 
triggered in recon-all.

Maybe somebody else has an idea...

Tim

> On March 4, 2020 at 4:47 PM Frank Chau  wrote:
>
>
> External Email - Use Caution
>
> Dear Tim,
>
> I have checked the orig.mgz file and nothing usual was found (please see the 
> attachment image)
>
> For downloading my orig.mgz: 
> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
>
> Regards
>
> Frank
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tim Schäfer 
> 
> Sent: 04 March 2020 23:27
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>
> External Email - Use Caution
>
> Dear Frank,
>
> if you search the log in your Dropbox for 'error', this comes up:
>
> 
> ERROR! FOV=284.000 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
> 
>
> Did you have a look at the orig.mgz?
>
> Best,
>
> Tim
>
>
> > On March 4, 2020 at 2:59 PM Frank Chau  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
> > "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited 
> > with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
> >
> > I've searched the email archive list and I found other researcher 
> > encountered same problem before. However, I am quite sure their root causes 
> > are not same as my case. 3 possible causes were found in the email archive 
> > which about "exited with ERRORS":
> >
> >   1.  The version of freesurfer (I have already used the latest 6.0.0 
> > version)
> >   2.  Hard disk space (My computer have enough hard disk space)
> >   3.  sharing folder between virtual machine and original platform. (I use 
> > freesurfer in Mac OS which do not have this problem)
> >
> > I uploaded the recon-all.log to my dropbox in case it's of any use.
> >
> >
> > 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >
> > 2) Platform: MAC OS X 10.11.6
> >
> > 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 
> > 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 
> > x86_64
> >
> > 4) recon-all.log, please download at:
> >
> > https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0
> >
> >
> >
> > 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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[Freesurfer] Tracula Inquiry

[Ledesma, Jason]

External Email - Use Caution

Hello,


I am having trouble carrying out Tracula on Freesurfer. See the following 
script (for confidentiality, patient's name has been replaced by XXX):


Admins-iMac:~ neurology$ export FREESURFER_HOME=/Applications/freesurfer

Admins-iMac:~ neurology$

Admins-iMac:~ neurology$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME   /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/subjects

MNI_DIR   /Applications/freesurfer/mni

Admins-iMac:~ neurology$ export 
SUBJECTS_DIR=/Applications/freesurfer/subjects/XXX

Admins-iMac:~ neurology$ cd /Applications/freesurfer/subjects/XXX

Admins-iMac:XXX neurology$ trac-all -prep -c XXX7.24.14Configfile

FSLDIR: Undefined variable.

Admins-iMac:XXX neurology$


My Config text file has the following info:


setenv SUBJECTS_DIR Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri

set dtroot = Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri

set subjlist = (XXX7.24.14)

set dcmroot = Applications/freesurfer/subjects/XXX/XXX7.24.14AXDWI

set dcmlist = ( MR0001.dcm )

set bvecfile = 
(Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bvec.txt)

set bvalfile = 
(Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bval.txt)

set doeddy = 1

set dorotbvecs = 1

set usemaskanat = 1

set threat = 0.3

set doregflt = 0

set doregbbr = 1

set doregmni = 1

set doregcvs = 0

set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

set pathlist = ( lh.cst_AS rh.cst_AS \

   lh.ilf_AS rh.ilf_AS \

   lh.unc_AS rh.unc_AS \

   fmajor_PP fminor_PP \

   lh.atr_PP rh.atr_PP \

   lh.cab_PP rh.cab_PP \

   lh.ccg_PP rh.ccg_PP \

   lh.slfp_PP rh.slfp_PP \

   lh.slft_PP rh.slft_PP )

set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)


Please advise. Thanks.



Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@labiomed.org



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[Freesurfer] Converting ANTs nonlinear transform to .m3z

[Ardesch, D.J.]

External Email - Use Caution

Dear FreeSurfer experts,

I am working on some monkey data and trying to get an accurate nonlinear 
transform to talairach space (talairach.m3z in the -careg stage). The problem 
is that the monkey brains look so different from the human brain that this 
registration ends up being very far off, even with an accurate talairach.lta.

As an alternative, I did a two-stage nonlinear registration using ANTs (first 
from subject to a macaque template and then from macaque template to 
talairach), which gives an accurate nonlinear transform. However, I can’t seem 
to convert this nonlinear transform file correctly from .nii.gz to the .m3z 
format that FreeSurfer needs to continue down the pipeline.

How would one go about converting the nonlinear transform from ANTs to a 
correct .m3z file?


Some other things I tried:


  *   I have tried a workaround in which I applied the inverse ANTs transform 
to the first frame of RB_all_2016-05-10.vc700.gca to get the talairach volume 
in subject space, and then ran mri_ca_register on that volume to obtain a 
talairach.m3z. That transform works but is still not accurate enough 
unfortunately.


  *   The nonlinear transform itself seems correct because when I apply it to 
the movable volume using ANTs the results are similar to:

mri_convert movable.mgz –apply_transform talairach.m3z -oc 0 0 0 
movable_in_talairach.mgz
where movable.mgz is the talairach volume in subject space and talairach.m3z is 
the transform made by mri_ca_register.
The dimensions, orientation, and voxel size of movable_in_talairach.mgz and my 
own transformed volume are identical.

Any help would be greatly appreciated!

Platform: MacOS Mojave
Version: FreeSurfer 6.0.0

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[Freesurfer] recon-all with errors

[Laboratorio de Neurociencia Funcional]

External Email - Use Caution

Dear Freesurfer experts,

After running the recon-all in one of my subjets, part of the temporal
lobe was partially excluded. Then, I tried to use the watershed
algorithm to be less agressive in the skull stripping
as follows:

recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001

The problem was solved in the brainmask.mgz but not in the cortical surfaces. To
handle this issue, I edited the white matter and run the recon-all
(-autorecon2-wm -autorecon3) without success. I also placed control
points but the
following error appeared after running
the recon-all -autorecon2-cp -autorecon3:

recon-all -s sub_001 existed with errors

I noted that white matter of this part of the temporal lobe has high
values (up to 132). What can I do to solve the problem with this subject?

Thank you in advance.

Best regards,
Marina
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Re: [Freesurfer] 8 Gb of ram

[Bruce Fischl]

I don't think our memory requirements change dramatically on a 
per-subject basis. The one exception might be topology fixing, but if it 
requires that much ram there are probably to many (or too large) defects to 
succeed in any case.


cheers
Bruce


On Thu, 5 Mar 2020, Ian wrote:



External Email - Use Caution

Hey guys.

I'm running Freesurfer on an AWS EC2 instance, in a docker container
(t3.large specifically.)

Would you expect 8Gb of ram to *always* be enough to run recon-all on a
280x280x240 T1 image?

The instance is running Ubuntu; the container image is based on Ubuntu; and
nothing else is being explicitly run on the instance while recon-all is
running.

Thanks,
Ian

--

Ian Hardingham



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[Freesurfer] 8 Gb of ram

[Ian]

   External Email - Use Caution


Hey guys.

I'm running Freesurfer on an AWS EC2 instance, in a docker container 
(t3.large specifically.)


Would you expect 8Gb of ram to *always* be enough to run recon-all on a 
280x280x240 T1 image?


The instance is running Ubuntu; the container image is based on Ubuntu; 
and nothing else is being explicitly run on the instance while recon-all 
is running.


Thanks,
Ian

--

*Ian Hardingham*


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Re: [Freesurfer] ubuntu: run freesurfer in two terminal

[Tim Schäfer]

External Email - Use Caution

For 2 subjects that is what you can do. 

If you have a lot more, I would suggest to have a look at GNU Parallel [1]. 
It's also available in the Ubuntu package system.

Best,

Tim

[1] https://www.gnu.org/software/parallel/

> On March 5, 2020 at 1:54 AM Bruce Fischl  wrote:
> 
> 
> sure, as long as you have more than one core. You can run them in the same
> terminal as long as you put & at the end of the line
> 
> On Thu, 5 Mar 2020, ZhangBo wrote:
> 
> > 
> > External Email - Use Caution
> > 
> > Hello FreeSurfer Developers,
> > 
> > My computer doesn't support cuda. To speed up data processing, could I open
> > two terminal, and in each of them, I first runing:
> > 
> > $> export FREESURFER_HOME=/usr/local/freesurfer
> > $> export FREESURFER_HOME=/SetUpFreeSurfer.sh
> > $> export SUBJECTS_DIR=/usr/local/freesurfer/subjects/
> > 
> > then running:
> > recon-all -s sub-01 -i sub-01_T1w.nii.gz -all (for terminal 1)
> > recon-all -s sub-02 -i sub-02_T1w.nii.gz -all (for terminal 2)
> > 
> > Thanks.
> > 
> > 
> > 
> > 
> >  
> > 
> > 
> > 
> >  
> > 
> > 
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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] mri_vol2surf produces invalid surface

[Shuntaro Aoki]

External Email - Use Caution

Thanks a lot.
Now I understand what was wrong and resolve it.


Shuntaro

2020年2月29日(土) 6:20 Douglas N. Greve :
>
> mri_vol2surf does not actually produce a surface, it produces a surface
> overlay (ie, a value for each vertex). You can to run recon-all to
> produce a surface
>
> On 2/27/2020 4:49 AM, Shuntaro Aoki wrote:
> >  External Email - Use Caution
> >
> > Dear mailing list,
> >
> > I was trying to convert a volume image to a freesurfer surface (as
> > gii) with `mri_vol2surf` for visualization, but ended up with invalid
> > surface data (i.e., a file not loadable by freeview).
> >
> > What I did was:
> >
> > ---
> > % mri_vol2surf --version
> > stable5
> > % mri_vol2surf --src ./sample_volume.nii.gz --regheader sample-sub
> > --hemi lh --out ./sample_vol2surf_lh.gii
> > ---
> >
> > Here, `sample_volume.nii.gz` is a volume image (such as a statistical
> > map) registered to an individual reference T1w image of subject
> > `sample-sub`, which was the input of recon-all for the subject.
> > The command completed without errors:
> >
> > ---
> > srcvol = ./sample_volume.nii.gz
> > srcreg unspecified
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = lh
> > reshape = 0
> > interp = nearest
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > Done loading volume
> > Computing registration from header.
> >Using /home/share/data/fmri/freesurfer/subjects/sample-sub/mri/orig.mgz
> > as target reference.
> > Reading surface
> > /home/share/data/fmri/freesurfer/subjects/sample-sub/surf/lh.white
> > Done reading source surface
> > Mapping Source Volume onto Source Subject Surface
> >   1 0 0 0
> > using old
> > Done mapping volume to surface
> > Number of source voxels hit = 31055
> > Writing to ./sample_vol2surf_lh.gii
> > Dim: 155685 1 1
> > ---
> >
> > Then I tried to open the resulting surface `sample_vol2surf_lh.gii`
> > with freeview (ver 1.0 build 2013-05-13) but it failed, saying "Failed
> > to load Surface".
> > I also got the following shell output:
> >
> > ---
> > mriseadGIFTIfile: mris is NULL! found when parsing file
> > /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii
> > MRISread failed
> > mriseadGIFTIfile: mris is NULL! found when parsing file
> > /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii
> > ---
> >
> > The output of `mris_info` is:
> >
> > ---
> > % mris_info sample_vol2surf_lh.gii
> > ==
> > gifti_image struct
> >  version= 1.0
> >  numDA  = 1
> > gim->meta nvpairs struct, len = 3 :
> >  nvpair: 'UserName' = 'aoki'
> >  nvpair: 'Date' = 'Thu Feb 27 17:32:40 2020'
> >  nvpair: 'gifticlib-version' = 'gifti library version 1.09, 28 June, 
> > 2010'
> >
> > gim->labeltable giiLabelTable struct, len = 0 :
> > --
> > gim->darray[0] giiDataArray struct
> >  intent  0 = NIFTI_INTENT_NONE
> >  datatype   16 = NIFTI_TYPE_FLOAT32
> >  ind_ord 1 = RowMajorOrder
> >  num_dim   = 1
> >  dims  = 155685, 0, 0, 0, 0, 0
> >  encoding3 = GZipBase64Binary
> >  endian  2 = LittleEndian
> >  ext_fname =
> >  ext_offset= 0
> > darray->meta nvpairs struct, len = 0 :
> >  data   = 
> >  nvals  = 155685
> >  nbyper = 4
> >  numCS  = 0
> > darray->ex_atrs nvpairs struct, len = 0 :
> > --
> > gifti_image struct
> >  swapped= 0
> >  compressed = 1
> >   -- darray totals: 1 MB
> > gim->ex_atrs nvpairs struct, len = 0 :
> > ==
> > ---
> >
> > I checked matching between voxels in the input volume and the surface
> > with the output of --srchit option and found the registration was
> > fine.
> >
> > I also tried mgh output but got another invalid file.
> >
> > ---
> > % mris_info sample_vol2surf_lh.mgh
> > ERROR: MRISread: file 'sample_vol2surf_lh.mgh' has 0 vertices!
> > Probably trying to use a scalar data file as a surface!
> >
> > No such file or directory
> > ---
> >
> > I would appreciate any advice on this.
> >
> > Regards,
> >
> >
> > Shuntaro
> >
> >
>
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-- 

Shuntaro C. Aoki, Ph.D.

Program-specific Researcher
Neuroinformatics group
Graduate School of Informatics
Kyoto University

s_a...@i.kyoto-u.ac.jp


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