[Freesurfer] mri_gtmpvc for partial volume

2018-08-24 Thread miracle ozzoude 
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Hello,

Can i specify a lookup table when using mri_gtmpvc? This is because I have
a non-freesurfer segmentation (MALPEM) and i would like to perform partial
volume on it without having to run freesurfer on the subject for PET
analysis. I have a lookup table for the segmentation.

I know mri_gtmpvc expects (?.ctab) file from the segmentation however, it
will require processing the subject with freesurfer and petsurfer. I only
want to use the partial volume command. How do I make it use the lookup
table i made rather than  ?.ctab file?

Thank you.

Best,
Paul
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Re: [Freesurfer] Unable to copy the license.txt file into $FREESURFER_HOME

2018-08-24 Thread Dicamillo, Robert 
Sent you a reply to your direct email, as attachment I wanted to send is too 
large for list.

- rob

On Aug 24, 2018, at 12:40 PM, Tsz Wai (Bentley) Lo 
mailto:lo...@smh.ca>> wrote:


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Hi FreeSurfer Developers,

I am attempting to copy my license.txt into $FREESURFER_HOME. I have already 
open a terminal window and define and environment variable called 
freesurfer_home but I am not sure where FreeSurfer home is. I am not sure how 
to source the set up script as well. I am on macOS high Sierra.

Bentley




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[Freesurfer] Convert mgh to gii

2018-08-24 Thread David.Mackarthy 
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Hi FS experts,
I ran surface based analysis between two groups. The final output "is 
cache.th13.pos.sig.cluster.mgh" I would like to convert this file to gii format 
using "mris_convert" I tried:

mris_convert -c cache.th13.pos.sig.cluster.mgh cache.th13.pos.sig.cluster.gii

Please what I am doing wrong?
Thanks for help
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[Freesurfer] Designing Constrats for 3 Group 1 Covariate Analysis

2018-08-24 Thread O'Dell, Ryan 
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Dear freesurfers,


I have what is likely a basic question but I'm new not only to FreeSurfer but 
contrast matrix design and group analysis as well, and was hoping for some 
help/clarification.


Basically I want to run a GLM on our structural/functional data in order to 
determine if there's any significant correlation between cortical thickness and 
cortical amyloid deposition (measured by PiB), factoring in any potential 
effects of APOE genotype (e3e3, e3e4, e4e4). This means I want to construct an 
FSGD file with a 3 groups (the 3 APOE genotypes) and 1 covariate (our 
calculated cortical composite PiB value) for this analysis. However, I'm 
struggling with the proper contrast designs which test the various hypotheses 
in such a setup.


Any answers, thoughts, or insights would be greatly appreciated. I know this 
type of analysis is also likely QDEC-able, but I think the FSGD approach would 
be more beneficial for my understanding of contrast matrix design. Please let 
me know if I've left out any information that could potentially help clarify my 
question/request.


Best,


Ryan O'Dell MD/PhD

PGY2 Psychiatry Resident, NRTP

Yale University

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[Freesurfer] Unable to copy the license.txt file into $FREESURFER_HOME

2018-08-24 Thread Tsz Wai (Bentley) Lo 
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Hi FreeSurfer Developers,

I am attempting to copy my license.txt into $FREESURFER_HOME. I have already 
open a terminal window and define and environment variable called 
freesurfer_home but I am not sure where FreeSurfer home is. I am not sure how 
to source the set up script as well. I am on macOS high Sierra.

Bentley




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Re: [Freesurfer] Error with mris_anatomical_stats

2018-08-24 Thread Davide Momi 
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Bruce,

this is the output:

mri_info wm.mgz

Volume information for wm.mgz

  type: MGH

dimensions: 256 x 256 x 256

   voxel sizes: 1.00, 1.00, 1.00

  type: UCHAR (0)

   fov: 256.000

   dof: 0

xstart: -128.0, xend: 128.0

ystart: -128.0, yend: 128.0

zstart: -128.0, zend: 128.0

TR: 8.21 msec, TE: 3.22 msec, TI: 450.00 msec, flip angle:
12.00 degrees

   nframes: 1

   PhEncDir: UNKNOWN

   FieldStrength: 0.00

ras xform present

xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
-6.3280

  : x_a =   0., y_a =   0., z_a =   1., c_a =
28.2400

  : x_s =   0., y_s =  -1., z_s =   0., c_s =
19.2471


talairach xfm :
/Users/davidemomi/Downloads/Broad_60_AV/60_AV/mri/transforms/talairach.xfm

Orientation   : LIA

Primary Slice Direction: coronal


voxel to ras transform:

   -1.   0.   0.   121.6720

0.   0.   1.   -99.7600

0.  -1.   0.   147.2471

0.   0.   0. 1.


voxel-to-ras determinant -1


ras to voxel transform:

   -1.  -0.  -0.   121.6720

   -0.  -0.  -1.   147.2471

   -0.   1.  -0.99.7600

   -0.  -0.  -0. 1.

thanks


Il giorno ven 24 ago 2018 alle ore 18:02 Bruce Fischl <
fis...@nmr.mgh.harvard.edu> ha scritto:

> can you run mri_info on it? And please include the full screen output
> including the command line that you run as well as what it produces.
>
> thanks
> Bruce
> On Fri,
> 24 Aug 2018, Davide Momi wrote:
>
> >
> > External Email - Use Caution
> >
> > Yes, I meant the second one and rh.aparc.annot (not lh) given that as
> you said I specified rh.
> >
> > As for the ls -l on wm.mgz this is the output:
> >
> > -rw---@ 1 davidemomi  staff  432151 Jun 13  2017 wm.mgz
> >
> > Thanks
> >
> >
> >
> > Il giorno ven 24 ago 2018 alle ore 17:35 Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> ha scritto:
> >   Hi Davide
> >
> >   do you mean $SUBJECTS_DIR/mri or $SUBJECTS_DIR/60_AV/mri? It
> should be the
> >   latter, not the former. Also, can you send us the output of ls -l
> on the
> >   wm.mgz? And finally, you probably want to use rh.aparc.annot not
> >   lh.aparc.annot since you specified rh on the command line
> >
> >   cheers
> >   Bruce
> >
> >
> > On Fri, 24 Aug 2018, Davide Momi wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Dear Bruce,
> >   >
> >   > thanks for your response.
> >   >
> >   > my SUBJECTS_DIR is set to:
>  /Users/davidemomi/Downloads/Broad_60_AV, which is actually
> >   where the
> >   > output of recon-all is located.
> >   >
> >   > the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory
> >   >
> >   > Thanks again
> >   >
> >   >
> >   >
> >   >
> >   > Il giorno ven 24 ago 2018 alle ore 16:49 Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> ha
> >   scritto:
> >   >   Hi Davide
> >   >
> >   >   does that file exist? What is your SUBJECTS_DIR set to?
> >   >
> >   >   cheers
> >   >   Bruce
> >   >   On Fri, 24 Aug 2018,
> >   >   Davide Momi wrote:
> >   >
> >   >   >
> >   >   > External Email - Use Caution
> >   >   >
> >   >   > Dear FreeSurfer,
> >   >   >
> >   >   > I have a problem when I use mris_anatomical_stats. It
> gives me an error saying
> >   that it
> >   >   couldn't read
> >   >   >  the input volume which is the wm.mgz file.
> >   >   > would you please help me how I should fix this problem?
> >   >   > this is the command which I used:
> >   >   >
> >   >   > mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh
> >   >   >
> >   >   > computing statistics for each annotation in
> label/lh.aparc.annot.
> >   >   >
> >   >   > reading volume
> /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz...
> >   >   >
> >   >   >
> mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1):
> could
> >   not open
> >   >   file
> >   >   >
> >   >   > mris_anatomical_stats: could not read input volume
> >   >   > /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz
> >   >   >
> >   >   >
> >   >   > Thanks in advance
> >   >   >
> >   >   >
> >   >   > Davide
> >   >   >
> >   >   >___
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> >   >   Freesurfer@nmr.mgh.harvard.edu
> >

Re: [Freesurfer] Error with mris_anatomical_stats

2018-08-24 Thread Bruce Fischl 
can you run mri_info on it? And please include the full screen output 
including the command line that you run as well as what it produces.


thanks
Bruce
On Fri, 
24 Aug 2018, Davide Momi wrote:




External Email - Use Caution

Yes, I meant the second one and rh.aparc.annot (not lh) given that as you said 
I specified rh. 

As for the ls -l on wm.mgz this is the output: 

-rw---@ 1 davidemomi  staff  432151 Jun 13  2017 wm.mgz

Thanks



Il giorno ven 24 ago 2018 alle ore 17:35 Bruce Fischl 
 ha scritto:
  Hi Davide

  do you mean $SUBJECTS_DIR/mri or $SUBJECTS_DIR/60_AV/mri? It should be the
  latter, not the former. Also, can you send us the output of ls -l on the
  wm.mgz? And finally, you probably want to use rh.aparc.annot not
  lh.aparc.annot since you specified rh on the command line

  cheers
  Bruce


    On Fri, 24 Aug 2018, Davide Momi wrote:

  >
  > External Email - Use Caution
  >
  > Dear Bruce, 
  >
  > thanks for your response. 
  >
  > my SUBJECTS_DIR is set to:  /Users/davidemomi/Downloads/Broad_60_AV, 
which is actually
  where the
  > output of recon-all is located. 
  >
  > the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory
  >
  > Thanks again 
  >
  >
  >
  >
  > Il giorno ven 24 ago 2018 alle ore 16:49 Bruce Fischl 
 ha
  scritto:
  >       Hi Davide
  >
  >       does that file exist? What is your SUBJECTS_DIR set to?
  >
  >       cheers
  >       Bruce
  >       On Fri, 24 Aug 2018,
  >       Davide Momi wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Dear FreeSurfer,
  >       >
  >       > I have a problem when I use mris_anatomical_stats. It gives me 
an error saying
  that it
  >       couldn't read
  >       >  the input volume which is the wm.mgz file.
  >       > would you please help me how I should fix this problem?
  >       > this is the command which I used: 
  >       >
  >       > mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh
  >       >
  >       > computing statistics for each annotation in 
label/lh.aparc.annot.
  >       >
  >       > reading volume 
/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz...
  >       >
  >       > 
mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1): could
  not open
  >       file
  >       >
  >       > mris_anatomical_stats: could not read input volume
  >       > /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz
  >       >
  >       >
  >       > Thanks in advance
  >       >
  >       >
  >       > Davide 
  >       >
  >       >___
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  >       contains patient information, please contact the Partners 
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e-mail
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Re: [Freesurfer] Error with mris_anatomical_stats

2018-08-24 Thread Davide Momi 
External Email - Use Caution

Yes, I meant the second one and rh.aparc.annot (not lh) given that as you
said I specified rh.

As for the ls -l on wm.mgz this is the output:

-rw---@ 1 davidemomi  staff  432151 Jun 13  2017 wm.mgz

Thanks



Il giorno ven 24 ago 2018 alle ore 17:35 Bruce Fischl <
fis...@nmr.mgh.harvard.edu> ha scritto:

> Hi Davide
>
> do you mean $SUBJECTS_DIR/mri or $SUBJECTS_DIR/60_AV/mri? It should be the
> latter, not the former. Also, can you send us the output of ls -l on the
> wm.mgz? And finally, you probably want to use rh.aparc.annot not
> lh.aparc.annot since you specified rh on the command line
>
> cheers
> Bruce
>
>
>   On Fri, 24 Aug 2018, Davide Momi wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Bruce,
> >
> > thanks for your response.
> >
> > my SUBJECTS_DIR is set to:  /Users/davidemomi/Downloads/Broad_60_AV,
> which is actually where the
> > output of recon-all is located.
> >
> > the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory
> >
> > Thanks again
> >
> >
> >
> >
> > Il giorno ven 24 ago 2018 alle ore 16:49 Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> ha scritto:
> >   Hi Davide
> >
> >   does that file exist? What is your SUBJECTS_DIR set to?
> >
> >   cheers
> >   Bruce
> >   On Fri, 24 Aug 2018,
> >   Davide Momi wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Dear FreeSurfer,
> >   >
> >   > I have a problem when I use mris_anatomical_stats. It gives me
> an error saying that it
> >   couldn't read
> >   >  the input volume which is the wm.mgz file.
> >   > would you please help me how I should fix this problem?
> >   > this is the command which I used:
> >   >
> >   > mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh
> >   >
> >   > computing statistics for each annotation in label/lh.aparc.annot.
> >   >
> >   > reading volume
> /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz...
> >   >
> >   >
> mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1):
> could not open
> >   file
> >   >
> >   > mris_anatomical_stats: could not read input volume
> >   > /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz
> >   >
> >   >
> >   > Thanks in advance
> >   >
> >   >
> >   > Davide
> >   >
> >   >___
> >   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.
> >
> >
> >___
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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
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> dispose of the e-mail.
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Re: [Freesurfer] mri_label2label dependencies

2018-08-24 Thread Krieger, Donald N. 
External Email - Use Caution

Dear freesurfers,

I didn't see a response to this but I might have missed it.
In any case it looks like it's working ok.
I found an error in what I was doing which was confusing things.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Krieger, Donald N.
Sent: Wednesday, August 22, 2018 8:35 PM
To: 'freesurfer@nmr.mgh.harvard.edu' 
Subject: [Freesurfer] mri_label2label dependencies


External Email - Use Caution
Dear freesurfers,

I am using mri_label2label with -regmethod volume .
The only other switches I am using are minimal as you can see below.


The thing is that none of the freesurfer stuff is in the srcsubject's directory.
Why is there no error message?
Where is it getting the stuff below the line: Src2TrgVolReg: ---   ?

Actually, I just need to know what to put into those directories so this 
function will work properly.
I see from the documentation that I need mri/transforms/talairach.xfm in both 
the src and trg subject directories.
Is there anything else that needs to be there?

mri_label2label --trgsubject 174 --srcsubject subNo1 --trglabel 
/dev/shm/32089_labels --srclabel /dev/shm/32089_tmp0-2 --regmethod volume

srclabel = /dev/shm/32089_tmp0-2
srcsubject = subNo1
trgsubject = 174
trglabel = /dev/shm/32089_labels
regmethod = volume

usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/usr/local/pkg/freesurfer//subjects
FREESURFER_HOME /usr/local/pkg/freesurfer/
Loading source label.
Found 33 points in source label.
Starting volumetric mapping 33 points
Src2TrgVolReg: -
0.963  -0.002  -0.044   0.330;
0.034   0.930  -0.328  -0.544;
0.044   0.285   0.919   13.268;
0.000   0.000   0.000   1.000;
  0  55. 17. 23.52.2444 9.6043 41.6544
  1  47. 1. 39.43.8696 -10.7903 51.4429
  2  52. -4. 28.49.1826 -11.6594 40.1300
  3  55. 17. 16.52.5536 11.8998 35.2230
  4  50. -10. 23.47.4912 -15.6659 33.7380
Writing label file /dev/shm/32089_labels 33
mri_label2label: Done


Thanks - Don


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Re: [Freesurfer] Error with mris_anatomical_stats

2018-08-24 Thread Bruce Fischl 

Hi Davide

do you mean $SUBJECTS_DIR/mri or $SUBJECTS_DIR/60_AV/mri? It should be the 
latter, not the former. Also, can you send us the output of ls -l on the 
wm.mgz? And finally, you probably want to use rh.aparc.annot not 
lh.aparc.annot since you specified rh on the command line


cheers
Bruce


 On Fri, 24 Aug 2018, Davide Momi wrote:



External Email - Use Caution

Dear Bruce, 

thanks for your response. 

my SUBJECTS_DIR is set to:  /Users/davidemomi/Downloads/Broad_60_AV, which is 
actually where the
output of recon-all is located. 

the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory

Thanks again 




Il giorno ven 24 ago 2018 alle ore 16:49 Bruce Fischl 
 ha scritto:
  Hi Davide

  does that file exist? What is your SUBJECTS_DIR set to?

  cheers
  Bruce
  On Fri, 24 Aug 2018,
  Davide Momi wrote:

  >
  > External Email - Use Caution
  >
  > Dear FreeSurfer,
  >
  > I have a problem when I use mris_anatomical_stats. It gives me an error 
saying that it
  couldn't read
  >  the input volume which is the wm.mgz file.
  > would you please help me how I should fix this problem?
  > this is the command which I used: 
  >
  > mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh
  >
  > computing statistics for each annotation in label/lh.aparc.annot.
  >
  > reading volume 
/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz...
  >
  > mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1): 
could not open
  file
  >
  > mris_anatomical_stats: could not read input volume
  > /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz
  >
  >
  > Thanks in advance
  >
  >
  > Davide 
  >
  >___
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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 
error
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Re: [Freesurfer] Error with mris_anatomical_stats

2018-08-24 Thread Davide Momi 
External Email - Use Caution

Dear Bruce,

thanks for your response.

my SUBJECTS_DIR is set to:  /Users/davidemomi/Downloads/Broad_60_AV, which
is actually where the output of recon-all is located.

the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory

Thanks again




Il giorno ven 24 ago 2018 alle ore 16:49 Bruce Fischl <
fis...@nmr.mgh.harvard.edu> ha scritto:

> Hi Davide
>
> does that file exist? What is your SUBJECTS_DIR set to?
>
> cheers
> Bruce
> On Fri, 24 Aug 2018,
> Davide Momi wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear FreeSurfer,
> >
> > I have a problem when I use mris_anatomical_stats. It gives me an error
> saying that it couldn't read
> >  the input volume which is the wm.mgz file.
> > would you please help me how I should fix this problem?
> > this is the command which I used:
> >
> > mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh
> >
> > computing statistics for each annotation in label/lh.aparc.annot.
> >
> > reading volume
> /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz...
> >
> > mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1):
> could not open file
> >
> > mris_anatomical_stats: could not read input volume
> > /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz
> >
> >
> > Thanks in advance
> >
> >
> > Davide
> >
> >___
> 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.
>
___
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Error with mris_anatomical_stats

2018-08-24 Thread Bruce Fischl 

Hi Davide

does that file exist? What is your SUBJECTS_DIR set to?

cheers
Bruce
On Fri, 24 Aug 2018, 
Davide Momi wrote:




External Email - Use Caution

Dear FreeSurfer,

I have a problem when I use mris_anatomical_stats. It gives me an error saying 
that it couldn't read
 the input volume which is the wm.mgz file.
would you please help me how I should fix this problem?
this is the command which I used: 

mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh

computing statistics for each annotation in label/lh.aparc.annot.

reading volume /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz...

mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1): could 
not open file

mris_anatomical_stats: could not read input volume
/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz


Thanks in advance


Davide 

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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] questions about hippocampus subfield error

2018-08-24 Thread Iglesias Gonzalez, Eugenio 
External Email - Use Caution

The subfield part never started. Recon-all died earlier.
Andrew: any ideas?

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 姜时泽 

Reply-To: Freesurfer support list 
Date: Friday, 24 August 2018 at 15:14
To: Freesurfer support list 
Subject: Re: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution
Hi Eugenio
I did not find the log file you mentioned. Attached is all log file within 
script directory. Would you please help me to figure out what was wrong?
Thank you so much
Best wishes
Shize




在 2018-08-24 15:50:44，"Iglesias Gonzalez, Eugenio"  写道：


External Email - Use Caution
I am really confused. There are no errors in the subfield module in that log.
Can you please send me the file hippocampal-subfields-T1.log, which should be 
found in the scripts directory (inside the subject’s directory)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 姜时泽 mailto:jiangshize1...@163.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 23 August 2018 at 23:02
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution
Hi Juan
Thank you for your kindly help. Attached is the log file with error. I am not 
sure if this is the file for hippocampus subfield segmentation.
Thank you very much
Shize





在 2018-08-24 05:08:35，"Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>> 写道：



External Email - Use Caution

Thanks! Can you please send us the log of the hippocampal subfield 
segmentation? It should be in the same directory as the recon-all log.

Cheers,

/E



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
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 姜时泽 mailto:jiangshize1...@163.com>>
Sent: Thursday, August 23, 2018 5:08:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution
Hi Eugenio,
Yes, If I run without the hippocampal subfield flag. Recon-all complete without 
any error. So I am confused what is wrong with this.
Thank you
Shize





在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>> 写道：



External Email - Use Caution

Hi Shize,

Does recon-all complete when you run it without the hippocampal subfield flag? 
It doesn’t look like an error in the subfield module to me …

Cheers,

/Eugenio



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

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





From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 姜时泽 mailto:jiangshize1...@163.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 23 August 2018 at 15:10
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] questions about hippocampus subfield error



External Email - Use Caution

Dear freesurfer experts,

I am trying to run recon-all with -hippocampal-subfields-T1 flag to get 
hippocampal subfield information. I tried many times but always finish with 
error. The MRI data is obtained from GE750 MRI machine. The resolution is 
1mm*1mm*1mm.

below is the commands I used to run freesurfer and attached is the recon-all 
log file.

recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 
-brainstem-structures -3T -qcache -all

I am not sure if there are something wrong with my inputs.

Thank you all

all the best

Shize






--

Shize Jiang
Fudan University,
Department of neurosurgery, Huashan Hospital, Shanghai Medical College
Shanghai,200032,P.R.China
Mobile: (86)18317079839
E-Mail: sjian...@fudan.edu.cn











[ge removed by sender.]























___
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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

Re: [Freesurfer] questions about hippocampus subfield error

2018-08-24 Thread 姜时泽 
External Email - Use Caution

Hi Eugenio
I did not find the log file you mentioned. Attached is all log file within 
script directory. Would you please help me to figure out what was wrong?
Thank you so much
Best wishes

Shize







在 2018-08-24 15:50:44，"Iglesias Gonzalez, Eugenio"  写道：


External Email - Use Caution

I am really confused. There are no errors in the subfield module in that log.

Can you please send me the file hippocampal-subfields-T1.log, which should be 
found in the scripts directory (inside the subject’s directory)?

Cheers,

/Eugenio

 

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

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

 

 

From:  on behalf of 姜时泽 

Reply-To: Freesurfer support list 
Date: Thursday, 23 August 2018 at 23:02
To: Freesurfer support list 
Subject: Re: [Freesurfer] questions about hippocampus subfield error

 

External Email - Use Caution

Hi Juan

Thank you for your kindly help. Attached is the log file with error. I am not 
sure if this is the file for hippocampus subfield segmentation.

Thank you very much

Shize







在 2018-08-24 05:08:35，"Iglesias Gonzalez, Eugenio"  写道：



External Email - Use Caution

Thanks! Can you please send us the log of the hippocampal subfield 
segmentation? It should be in the same directory as the recon-all log.

Cheers,

/E

 

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 姜时泽 

Sent: Thursday, August 23, 2018 5:08:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] questions about hippocampus subfield error

 

External Email - Use Caution

Hi Eugenio,

Yes, If I run without the hippocampal subfield flag. Recon-all complete without 
any error. So I am confused what is wrong with this.

Thank you

Shize







在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio"  写道：



External Email - Use Caution

Hi Shize,

Does recon-all complete when you run it without the hippocampal subfield flag? 
It doesn’t look like an error in the subfield module to me …

Cheers,

/Eugenio

 

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

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

 

 

From:  on behalf of 姜时泽 

Reply-To: Freesurfer support list 
Date: Thursday, 23 August 2018 at 15:10
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] questions about hippocampus subfield error

 

External Email - Use Caution

|
|

Dear freesurfer experts,

I am trying to run recon-all with -hippocampal-subfields-T1 flag to get 
hippocampal subfield information. I tried many times but always finish with 
error. The MRI data is obtained from GE750 MRI machine. The resolution is 
1mm*1mm*1mm. 

below is the commands I used to run freesurfer and attached is the recon-all 
log file.

recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 
-brainstem-structures -3T -qcache -all

I am not sure if there are something wrong with my inputs.

Thank you all

all the best

Shize







--

Shize Jiang
Fudan University,
Department of neurosurgery, Huashan Hospital, Shanghai Medical College
Shanghai,200032,P.R.China
Mobile: (86)18317079839
E-Mail: sjian...@fudan.edu.cn











|
|
|

|





 






 






 ___
Freesurfer mailing list
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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] Error with mris_anatomical_stats

2018-08-24 Thread Davide Momi 
External Email - Use Caution

Dear FreeSurfer,

I have a problem when I use mris_anatomical_stats. It gives me an
error saying that it couldn't read the input volume which is the
wm.mgz file.
would you please help me how I should fix this problem?

this is the command which I used:

mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh

computing statistics for each annotation in label/lh.aparc.annot.

reading volume /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz...

mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1):
could not open file

mris_anatomical_stats: could not read input volume
/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz


Thanks in advance

Davide
___
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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 error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] questions about hippocampus subfield error

2018-08-24 Thread Iglesias Gonzalez, Eugenio 
External Email - Use Caution

I am really confused. There are no errors in the subfield module in that log.
Can you please send me the file hippocampal-subfields-T1.log, which should be 
found in the scripts directory (inside the subject’s directory)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 姜时泽 

Reply-To: Freesurfer support list 
Date: Thursday, 23 August 2018 at 23:02
To: Freesurfer support list 
Subject: Re: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution
Hi Juan
Thank you for your kindly help. Attached is the log file with error. I am not 
sure if this is the file for hippocampus subfield segmentation.
Thank you very much
Shize




在 2018-08-24 05:08:35，"Iglesias Gonzalez, Eugenio"  写道：


External Email - Use Caution

Thanks! Can you please send us the log of the hippocampal subfield 
segmentation? It should be in the same directory as the recon-all log.

Cheers,

/E



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
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 姜时泽 mailto:jiangshize1...@163.com>>
Sent: Thursday, August 23, 2018 5:08:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] questions about hippocampus subfield error


External Email - Use Caution
Hi Eugenio,
Yes, If I run without the hippocampal subfield flag. Recon-all complete without 
any error. So I am confused what is wrong with this.
Thank you
Shize




在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>> 写道：


External Email - Use Caution

Hi Shize,

Does recon-all complete when you run it without the hippocampal subfield flag? 
It doesn’t look like an error in the subfield module to me …

Cheers,

/Eugenio



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

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





From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 姜时泽 mailto:jiangshize1...@163.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 23 August 2018 at 15:10
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] questions about hippocampus subfield error



External Email - Use Caution

Dear freesurfer experts,

I am trying to run recon-all with -hippocampal-subfields-T1 flag to get 
hippocampal subfield information. I tried many times but always finish with 
error. The MRI data is obtained from GE750 MRI machine. The resolution is 
1mm*1mm*1mm.

below is the commands I used to run freesurfer and attached is the recon-all 
log file.

recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 
-brainstem-structures -3T -qcache -all

I am not sure if there are something wrong with my inputs.

Thank you all

all the best

Shize





--

Shize Jiang
Fudan University,
Department of neurosurgery, Huashan Hospital, Shanghai Medical College
Shanghai,200032,P.R.China
Mobile: (86)18317079839
E-Mail: sjian...@fudan.edu.cn










[age removed by sender.]















___
Freesurfer mailing list
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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.