Re: [Freesurfer] Thalamic Nuclei segmentation results

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Vasudev,

What lookup table are you using to visualize the results? Are you using 
FreeView from the development version, and visualizing the segmentation with 
the default lookup table?

Cheers,

/Eugenio


Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Dev vasu 

Sent: Tuesday, October 9, 2018 10:06:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Thalamic Nuclei segmentation results


External Email - Use Caution

Dear all,

I have used Freesurfer pipeline for Thalamic  Nuclei segmentation, the results 
of segmentation appear to be very poor, i am annexing the results , please 
kindly review if there is any thing wrong with the segmentation results.


Thanks
Vasudev
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Thalamic Nuclei segmentation results

[Dev vasu]

External Email - Use Caution

Dear all,

I have used Freesurfer pipeline for Thalamic  Nuclei segmentation, the
results of segmentation appear to be very poor, i am annexing the results ,
please kindly review if there is any thing wrong with the segmentation
results.


Thanks
Vasudev
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all terminated in middle : continuing an analysis of an existing subject

[Hoopes, Andrew]

Hi Vasudev, if you're using freesurfer 6.0 or the development version, you can 
update the recon-all makefile by running the following (this might require 
sudo):

cd $FREESURFER_HOME/bin
mv recon-all.makefile recon-all.makefile.backup
curl 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/recon-all.makefile
 -o recon-all.makefile
chmod +x recon-all.makefile

Now, you should be able to successfully use the "-make all" flag with 
recon-all, which will start it from where it was terminated.

best
Andrew


On 10/7/18, 11:25 AM, "Bruce Fischl"  wrote:

Hi Vasudev

there is a patch to recon-all that fixes the -make all functionality, 
that should start wherever you left off.  Andrew: can you post the location 
of the makefile patches?

thanks
Bruce


On Sun, 7 Oct 
2018, Dev vasu wrote:

> 
> External Email - Use Caution
> 
> Dear all,
> 
> I was trying to run recon-all, the pipeline terminated in middle now i 
would like to know if there
> is any way i can restart it from the point where it was terminated?.
> 
> 
> Thanks
> Vasudev
> 
>


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] masking cortical thickness

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

Use the --outmask option

On 10/07/2018 08:59 AM, N Saf wrote:
>
> External Email - Use Caution
>
> Dear Douglos,
>
> I did not understand how to use mri_label2label with the mask 
> option(there is srcmask options not mask alone !). I extract my labels 
> and as you explained I wanted to create i.e. binary mask of 
> rh.fusiform.label  with mri_label2label :
>   mri_label2label  --srcsubject case1 --srclabel rh.fusiform.label 
> --trgsubject case1 --trglabel outputlabel.mgh --regmethod surface 
> --hemi rh
>
> but it creats another label file not binary with mgh format I did not 
> get how can I create mybinary.mgh mask in order to use in third 
> command "mri_binarize --i lh.thickness --mask youmask.mgh --o 
> lh.thickness.masked.mgh"
>
> would you please help me with this, it would be a great favor.
>
> Best regards,
> Nazanin
>
> On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Yes, that should work. You can create a mask by breaking the
> annotation
> into labels (mri_annotation2label), then converting the label into a
> binary mask (mri_label2label with --mask option), then
> mri_binarize --i
> lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh
>
>
> On 07/30/2018 01:47 AM, N Saf wrote:
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer Experts,
> >
> > I wonder how can I show the cortical thickness surface on just one
> > region of my interest in Freeview.  assume that I want to see the
> > thickness surface of one of the regions in DKTatlas. does it
> work if I
> > make a binary mask of that specific region on
> aparcDKTatlas.annot and
> > then multiply it to the ?h.thickness surface ?? any help will be
> > appreciated.
> >
> > Best Regards,
> > Nazanin
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@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@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] nu_correct disk i/o issues

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

BTW, this should not be a problem in the next version

On 10/07/2018 08:29 AM, Jasper van den Bosch wrote:
>
>
> Michael, I can't thank you enough.
>
> Knowing that it writes to /tmp made all the difference.
> In my case I mounted an external directory on /tmp instead of the 
> sessiondir approach, but it now runs fine.
> Jasper
>
> On Fri, 5 Oct 2018 at 23:47, Michael Krause  > wrote:
>
> Dear *,
>
> we also run Freesurfer on a cluster and are starting to use
> singularity, so
> naturally I'm curious about this issue.
>
> I was able to reproduce the error with a clean singularity run (-c
> -e).
> Then, I rebuilt a container to start nu_correct with "strace -f -e
> open,write" and I believe I found the problem:
>
> [pid 35994]
> open("/subs/testsub/mri/tmp.mri_nu_correct.mni.35410/nu1.imp",
> O_RDONLY) = 3
> [pid 35994] open("/tmp/minc-qKdMD4", O_RDWR|O_CREAT|O_EXCL, 0600) = 5
> [pid 35994] open("/tmp/minc-qKdMD4", O_RDWR|O_CREAT|O_TRUNC, 0666) = 5
> [pid 35994] write(5, "\0\0\0\0\0\0\0\0", 8) = 8
> [pid 35994] write(5,
> "CDF\1\0\0\0\0\0\0\0\n\0\0\0\3\0\0\0\6xspace\0\0\0\0\1\0"...,
> 8192) = 8192
> [pid 35994] write(5,
> 
> "|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0"...,
> 8192) = 8192
> [...]
> [pid 35994] write(5,
> 
> "|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0"...,
> 8192) = -1 ENOSPC (No space left on device)
> [pid 35994] write(2, "ncendef: ", 9ncendef: )    = 9
> [pid 35994] write(2, "ncid 5", 6ncid 5)       = 6
> [pid 35994] write(2, ": No space left on device", 25: No space left on
> device) = 25
>
>
> So there are two issues here I think:
>
> 1) nu_correct is saving things to /tmp when it could just use ./tmp
> 2) the singularity default for "sessiondir max size" is 16MB,
> which includes
> /tmp, is too small for the minc-tmp files
>
> I changed the value from 16 to 1024 and it passed the nu_correct step.
>
> cheers,
> Michael
>
> On 10/5/18 5:57 PM, Greve, Douglas N.,Ph.D. wrote:
> > Not that I know of, but this is not a native FS script, it comes
> from the
> > MNI, so it could be doing something we don't understand. Can you
> do an
> > experiment for us? Can you run it outside of the container using
> reprozip
> > (or something equivalent) to see all the files it touches?
> >
> > On 10/5/18 5:31 AM, Jasper van den Bosch wrote:
> >>
> >> External Email - Use Caution
> >>
> >> We are trying to run recon_all inside an fmriprep singularity
> container,
> >> but are running into an issue with nu_correct. It says it
> cannot write to
> >> disk, however there is plenty of space on the tmpdir and output
> dir. Does
> >> this script try to write to any other locations? Because this
> would fail
> >> inside the container, where each writable location has to be
> 'mounted'.
> >>
> >> Error message:
> >>
> >> ncendef: ncid 5: No space left on device
> >> Error outputting volume: possibly disk full?
> >> nu_evaluate: crashed while running evaluate_field (termination
> status=139)
> >> nu_correct: crashed while running nu_evaluate (termination
> status=65280)
> >> ERROR: nu_correct
> >>
> >> Command ran:
> >>
> >> nu_correct -clobber ./tmp.mri_nu_correct.mni.1121/nu0.mnc
> >> ./tmp.mri_nu_correct.mni.1121/nu1.mnc -tmpdir
> >> ./tmp.mri_nu_correct.mni.1121/0/ -iterations 1000 -distance 50
> >> [xxx@.cluster:/data/BIDS/derivatives/freesurfer/sub-1/mri/]
> >> [2018-10-04 14:59:29] running:
> >>   /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log
> -sharpen 0.15
> >> 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask
> -nonotify -b_spline
> >> 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir
> >> ./tmp.mri_nu_correct.mni.1121/0/
> ./tmp.mri_nu_correct.mni.1121/nu0.mnc
> >> ./tmp.mri_nu_correct.mni.1121/nu1.imp
> >>
> >>
> >> this issue at the fmriprep
> >> repo: https://github.com/poldracklab/fmriprep/issues/1308
> >> possibly related:
> https://github.com/freesurfer/freesurfer/issues/462
> >>
> >> Many thanks for any advice,
> >> Jasper van den Bosch
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> 
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
>
> External 

Re: [Freesurfer] Extract individual vertex thickness values from cortical parcellations

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

You can use matlab. read_curv.m will read in a thickness. 
read_annotation.m will read in the annotation. Look at the help in both 
for more info

On 10/06/2018 11:36 AM, lindsay hanford wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Community,
>
> I am looking for a way to extract thickness values at the level of 
> each vertex from Freesurfer atlas-based parcellated regions 
> (aparc.annot), or more generally lobes. Is this possible?
>
> Using mri_segstats I know it is possible to get more general metrics 
> such as min, max and average thickness values, and # of voxels. Is it 
> possible to use an annot file to read out the raw thickness values?
>
> This post was the closest I could find to answering my question, 
> however, this was at the group level and not specified for parcellated 
> regions. 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022097.html
>
> Thank you in advance,
>
> Lindsay
>
> -- 
> *Lindsay Hanford, PhD*
> *The Buckner Laboratory**|**Harvard University*
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"

[Bruce Fischl]

Hi Maedeh

the surface file should be the one that defines the common coordinate 
system (usually sphere.reg) and the annotation should refer to a file in 
the subject's label dir. Every subject in your list must have both files.


cheers
Bruce

On Tue, 9 Oct 2018, Maedeh Khalilian wrote:



External Email - Use Caution

Dear Dr.Bruce Fischl
Thank you very much for your great sense of responsibility.
Sure, i have sent you a zip file named "Maedeh_results"(it was a rather big 
sized one so i had to
send it through Wetranser). Hope you have received it.
However, a general question is that, according to freesurfer help the required 
arguments for
"mris_ca_train" are :
mris_ca_train [options]  ... 


as it seems it gets one surf file(e.g sphere.reg),and one annotation file, but 
several subjects...so
what does this surface file refer to?should i make an average of all subjects' 
.reg files? and also
for the annotation file ! just one .annot is enough or i have to make an 
average of several
annotation files?
if yes, how should i do that?
i would be grateful if you could help me.
Best regards
Maedeh,
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Talairach failed in monkey brain

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

The file passed to --reg should be a registration file. This is a text file 
with the transformation matrix and a few other things, not a volume file.

On 10/8/18 5:28 PM, Frehiwot Woldeyes wrote:

External Email - Use Caution

Hello Freesurfers,

I was attempting to reconstruct a monkey brain, i encountered an error during 
talairach registration step, i have used tkregister2 to manually edit the 
registration but i have gotten error there too:

tkregister2 --targ 
/usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --mov 
/usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --reg 
/usr/local/freesurfer/subjects/A004_crop.mhd.nii
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
target  volume /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii
movable volume /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii
reg file   /usr/local/freesurfer/subjects/A004_crop.mhd.nii
LoadVol1
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
regio_read_register(): No such file or directory
Could not open /usr/local/freesurfer/subjects/A004_crop.mhd.nii
ERROR: reading /usr/local/freesurfer/subjects/A004_crop.mhd.nii

Do you have any thoughts on how to troubleshoot this one?

Regards,
frehiwot



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Recon-all with/without T2 give the same stats

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

But are the lh.thickness files the same or different?

On 10/9/18 1:46 AM, Jianzhong Chen wrote:

External Email - Use Caution

Hi Dr. Greve,

I checked the lh.aparc.stats and rh.aparc.stats, the thicknesses (and the other 
measures like volume and area) are all the same.

Thanks,
Jianzhong

Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> 
于2018年10月9日周二 上午10:16写道：
The aseg.stats should be the same since that does not make reference to the 
surfaces. The aparc stats should have been different because the thickness 
should have been different. Can you check whether the thickness files are 
different?

On 10/8/18 9:39 AM, Jianzhong Chen wrote:

External Email - Use Caution

Dear All,

I tried recon-all with/without T2 image using FS 5.3.0. Then I found that the 
aseg stats and aparc stats with/without T2 are exactly the same. When I check 
the pial surfaces, I can see that they are very similar but not the same. So is 
it reasonable to see exactly the same stats?
An example of the pial surfaces with/without T2 is attached here. The red line 
is lh.pial with T2 and the yellow line is the lh.pial without T2
My command for recon-all with T2 is: recon-all -s ${subject} -i T1.nii -all -T2 
T2.nii -T2pial -sd ${T2_dir}
My command for recon-all without T2 is: recon-all -s ${subject} -i T1.nii -all 
-sd ${T1_dir}

Thanks,
Jianzhong



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"

[Maedeh Khalilian]

External Email - Use Caution

Dear Dr.Bruce Fischl
Thank you very much for your great sense of responsibility.
Sure, i have sent you a zip file named "Maedeh_results"(it was a rather big 
sized one so i had to send it through Wetranser). Hope you have received it.
However, a general question is that, according to freesurfer help the 
required arguments for "mris_ca_train" are :
mris_ca_train [options] 
 ... 

 as it seems it gets one surf file(e.g sphere.reg),and one annotation file, 
but several subjects...so what does this surface file refer to?should i make 
an average of all subjects' .reg files? and also for the annotation file ! 
just one .annot is enough or i have to make an average of several annotation 
files?
if yes, how should i do that?
i would be grateful if you could help me.
Best regards
Maedeh,___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] m.khalil...@sutech.ac.ir sent you files via WeTransfer

[WeTransfer]

External Email - Use Caution

m.khalil...@sutech.ac.ir sent you some files

1 file, 378 MB in total
・ Will be deleted on 16 October, 2018


Download link:
https://wetransfer.com/downloads/9370a847d04b46d6fcbc4faec24f094e20181009110257/83dcd2124cf5da491c194f833e0c804c20181009110257/327c62


Message:
Dear Dr.Bruce Fischl
Thank you very much for your great sense of responsibility.
Sure, i have attached a zip file named "Maedeh_results"(it was a rather big 
sized one so i
had to send it through Wetranser). It contains my initial annotation files(as 
the input of
'mris_ca-train') by which i have made my atlas(?h.Desikan100.annot), my  
atlases for both
hemispheres(?hDesikan100.gcs), a color LUT, my subject directory "test1" which 
i have used
as the input of "mris_ca_train", another subject diectory "subj1", on which i 
have used to
test my atlas, and finally my results "?h.finalDesikan100.annot" .(actually the 
result of
applying my atlas on subj1)
i myself guess that the main problem is that i am using just one subject as the 
input of
"mris_ca_train", but i dunno how to get multiple subjects...
that would be perfect if you could help me.
Cheers
Maedeh.



1 file

Maedeh_results.zip


[Get more out of WeTransfer, get 
Plus](https://wetransfer.com/plus?trk=WT201704_email_campaign=WT_email_tracking_content=general_medium=plus_footer_ad_link_source=notify_recipient_email)



About WeTransfer: https://wetransfer.com/about
Help: https://wetransfer.zendesk.com/hc/en-us
Legal: https://wetransfer.com/legal/terms


To make sure our emails arrive, please add nore...@wetransfer.com to [your 
contacts](https://wetransfer.zendesk.com/hc/en-us/articles/204909429).

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer