Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256

[Juhyoung Ryu]

Hi Bruce,

Yes I’m using v6.0.
I found that there is -hires flag in version 6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon 
)
and i included that;  recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 
T2_bfc.nii -T2pial -all -cw256


Thanks,
Juhyoung

> On Jul 28, 2017, at 2:19 AM, Bruce Fischl  wrote:
> 
> Hi  Juhyoung
> 
> what FS version are you running with? If 6.0 you want to include the -highres 
> flag
> 
> cheers
> Bruce
> 
> 
> 
> On Thu, 27 Jul 2017, juhyoung Ryu wrote:
> 
>> Hi experts,
>> I'm trying to surface reconstruction using high-resolution T1 and T2 data
>> using freesurfer version 6
>> So I typed like this: 
>> recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial
>> -all
>> and that excited with errors like this;
>> \n
>> ERROR! FOV=272.000 > 256
>> Include the flag -cw256 with recon-all!
>> Inspect orig.mgz to ensure the head is fully visible.
>> \n
>> So I added -cw256 flag and run the command line again (recon-all -subject
>> ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all -cw256). But
>> the result is same.
>> I'd appreciate any suggestion.
>> Thank you,
>> Juhyoung
> ___
> 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


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] Is it possible to run a conjunction analysis on longitudinal sMRI data in Freesurfer?

[Douglas N Greve]

If you have two sig maps, then use mri_concat with the --conjunct option


On 07/27/2017 02:37 PM, Jennifer Legault wrote:
> Hi Freesurfer experts,
>
> I'm wondering if it's possible to do a conjunction analysis on sMRI 
> data in Freesurfer.  I would like to compare longitudinal results from 
> 2 experimental training groups and 1 control, where I can examine: 1) 
> which regions underwent structural changes in both of the experimental 
> groups as compared to the control and 2) experimental 
> condition-specific changes between the groups when accounting for the 
> normal amount of change expected (the controls).  Of course, if you 
> know of a better analysis to run to examine these questions, any 
> feedback would be greatly appreciated.
>
> I have previously preprocessed the data using Freesurfer's 
> longitudinal pipeline and I've run univariate LMEs using Freesurfer to 
> compare each of the experimental groups to the control group 
> separately.  Do you know if I can I use mri_concat with the --conjunct 
> option using the .sig files from the LME analyses, given that these 
> are structural MRI data?  I've only ever seen these analyses being 
> done with fMRI data.
>
> Thank you for taking the time to read this email.
>
> Best,
>
> Jennifer Legault
> -- 
> Jennifer Legault
> Ph.D candidate, Neuroscience
> Brain, Language, and Computation Lab
> The Pennsylvania State University
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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] Is it possible to run a conjunction analysis on longitudinal sMRI data in Freesurfer?

[Jennifer Legault]

Hi Freesurfer experts,

I'm wondering if it's possible to do a conjunction analysis on sMRI data in
Freesurfer.  I would like to compare longitudinal results from 2
experimental training groups and 1 control, where I can examine: 1) which
regions underwent structural changes in both of the experimental groups as
compared to the control and 2) experimental condition-specific changes
between the groups when accounting for the normal amount of change expected
(the controls).  Of course, if you know of a better analysis to run to
examine these questions, any feedback would be greatly appreciated.

I have previously preprocessed the data using Freesurfer's longitudinal
pipeline and I've run univariate LMEs using Freesurfer to compare each of
the experimental groups to the control group separately.  Do you know if I
can I use mri_concat with the --conjunct option using the .sig files from
the LME analyses, given that these are structural MRI data?  I've only ever
seen these analyses being done with fMRI data.

Thank you for taking the time to read this email.

Best,

Jennifer Legault
-- 
Jennifer Legault
Ph.D candidate, Neuroscience
Brain, Language, and Computation Lab
The Pennsylvania State University
___
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.

Re: [Freesurfer] problem with bedpostx

[Yendiki, Anastasia]

Hi – Is this on ubuntu by any chance? I remember it cropping up a while ago, 
and I think you had to change something in the first line of the script. It 
should be in the archives.

From: 
>
 on behalf of "Lars M. Rimol" >
Reply-To: Freesurfer support list 
>
Date: Thursday, July 27, 2017 at 1:43 PM
To: FS maling list 
>
Subject: [Freesurfer] problem with bedpostx

Hi,

Running trac-all -bedp and getting an error message I've never seen before. I'm 
running it on a desktop, not a cluster, which it warns agains - but it should 
still run, shouldn't it?


larsrim:~/lbkabel/tbi/morfometri_test$ trac-all -bedp -c 
DWI/jobscripts/d1_1001_local.dmrirc

INFO: SUBJECTS_DIR is /home/larsrim/lbkabel/tbi/morfometri_test
INFO: Diffusion root is 
/home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local
Actual FREESURFER_HOME /usr/local/freesurfer
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 
/home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local/1001_c1/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131: 
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected





Sincerely yours,

Lars M. Rimol, PhD
Senior Researcher
Norwegian Advisory Unit for Functional MRI
Department of Radiology
St. Olav's University Hospital
7006 Trondheim
Norway

___
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] problem with bedpostx

[Lars M. Rimol]

Hi,

Running trac-all -bedp and getting an error message I've never seen before.
I'm running it on a desktop, not a cluster, which it warns agains - but it
should still run, shouldn't it?


larsrim:~/lbkabel/tbi/morfometri_test$ trac-all -bedp -c
DWI/jobscripts/d1_1001_local.dmrirc

INFO: SUBJECTS_DIR is /home/larsrim/lbkabel/tbi/morfometri_test
INFO: Diffusion root is
/home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local
Actual FREESURFER_HOME /usr/local/freesurfer
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2
/home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local/1001_c1/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected





Sincerely yours,

Lars M. Rimol, PhD
Senior Researcher
Norwegian Advisory Unit for Functional MRI
Department of Radiology
St. Olav's University Hospital
7006 Trondheim
Norway
___
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.

Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates

[Douglas N Greve]

Hard to say whether the coords are right or not. You can run tksurfer 
and look at the coords in and around your region to see whether they are 
reasonable. The -1s need to go into the label that is used as input the 
mri_label2label. mri_label2label will assign vertex numbers based on the 
coordinates. Those vertex numbers are needed in order to load it on the 
surface


On 07/26/2017 11:08 PM, Florence Campana wrote:
> Hi Doug,
>
> Thank you for your reply. I computed the tkRAS coordinates using the 
> formula TkRAS = Torig*[C R S 1]’. It returns me coordinates such as: 
> [113, -119,88], [105, -103, 96]. I wonder whether such tkRAS 
> coordinates are normal since
> in label files obtained by saving ROI upon a certain threshold in 
> tksurfer, the coordinates seem fairly different: non integers, and in 
> different ranges e.g. [-36.806  -18.293  64.462], [-21.393  -61.263 
>  8.910]) etc.
>
> However, when I create a label file (via write_label.m) with -1 in the 
> first column and with the TkRAS coordinates that I computed in the 
> columns 2,3,4 , and then via tksurfer load this label and then save 
> the selected label, I obtain a new label with R A S coordinates as 
> [34.198  -48.599  29.835], [35.364  -45.689  31.179], i.e. similar to 
> the one that I have in my ROI label files.
>
> Could you please help me to figure out what my tkRAS values (e.g.[113, 
> -119,88], [105, -103, 96) correspond to, versus the ones returned by 
> tksurfer ([34.198  -48.599  29.835], [35.364  -45.689  31.179])?
>
> I hope that it makes sense. Thank you so much!
>
> Florence
>
>
>
>> *From:* Douglas Greve > >
>> *Date:* July 24, 2017 at 4:06:25 PM EDT
>> *To:* > >
>> *Subject:* *Re: [Freesurfer] converting vertex numbers in .label 
>> files to R, A, S coordinates*
>> *Reply-To:* Freesurfer support list > >
>>
>> Try using mri_label2label with the --paint option. I think the vertex 
>> numbers need to be -1 (not random numbers). You will also need to 
>> convert the RAS to "tkregisterRAS", one of our internal coordinate 
>> systems. See 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems, you'll 
>> need to do the inverse of case #1.
>>
>>
>> On 7/19/17 12:28 PM, Li Guo wrote:
>>> /Dear Freesurfer experts,/
>>> /
>>> /
>>> /My question concerns the .label files and the correspondence 
>>> between the vertex numbers (in the first column) and the R,A,S 
>>> coordinates./
>>> /
>>> /
>>> /I have the R,A,S coordinates of voxels that I want to display on 
>>> the surface. For this purpose, I created a label file with the R,A,S 
>>> coordinates (col 2,3,4) and random vertex ID in the col 1 (since I 
>>> do not know what is the vertex ID for a given R,A,S coordinate). 
>>> I displayed the content of the label file via tksurfer. However, 
>>> tksurfer reads vertex ID, not R,A,S coordinates. /
>>> /
>>> /
>>> /I wonder whether anyone knows about a function computing the vertex 
>>> ID based on the R,A,S coordinates, or an alternative solution 
>>> to represent the vertices on the surface based on the voxel 
>>> coordinates--and the registration file I assume?
>>> /
>>> /
>>> /
>>> /Thank you very much!/
>>> /
>>> /
>>> /Best/
>>> /Li Guo & Florence Campana/
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256

[Bruce Fischl]

Hi  Juhyoung

what FS version are you running with? If 6.0 you want to include the 
-highres flag


cheers
Bruce



On Thu, 27 Jul 2017, juhyoung Ryu wrote:




Hi experts,


I'm trying to surface reconstruction using high-resolution T1 and T2 data
using freesurfer version 6
So I typed like this: 
recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial
-all


and that excited with errors like this;

\n

ERROR! FOV=272.000 > 256

Include the flag -cw256 with recon-all!

Inspect orig.mgz to ensure the head is fully visible.

\n


So I added -cw256 flag and run the command line again (recon-all -subject
${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all -cw256). But
the result is same.



I'd appreciate any suggestion.


Thank you,

Juhyoung


___
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.

Re: [Freesurfer] negative header after preproc-sess

[Douglas N Greve]

Yes, it is on my to-do list :)


On 07/27/2017 11:42 AM, Christopher Markiewicz wrote:
> Hi Doug,
>
> I wonder if there's a plan to move to NIfTI-2 as the default encoding for 
> .nii(.gz) images that would can't be encoded in a standard-conforming 
> NIfTI-1? I believe all of the major packages support NIfTI-2 in their latest 
> releases (with the possible exception of ANTs, which I don't believe handles 
> surface data in any event).
>
> Chris Markiewwicz
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas Greve 
> 
> Sent: Wednesday, July 5, 2017 7:07:50 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] negative header after preproc-sess
>
> When the nifti standard was adopted, they used a short int to represent the 
> dimensions. Unfortunately, this only allows for a maximum dimension of 32k, 
> which is not big enough for surfaces. So I hacked the FS nifti format to put 
> a -1 as the first dim at which point the FS code will go to another place in 
> the header to get the spatial dimensions. It is possible to reshape the 
> spatial dimensions as long as the largest prime factor is less than 32k (see 
> mri_surf2surf with --reshape option). Other than that, you might ask the 
> nibabel people to program the same hack.
>
> On 6/25/17 6:48 AM, Bai Haohao wrote:
> Hello Freesurfer experts,
>
> I am running my data with preproc-sess to project my func data to individual 
> anatomy file, and the command shows as below:
>
> preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh -fwhm 0 -per-run 
> -force
>
> And the subjectname point to the subject dir that created after recon-all.
>
> After the running completed, I try to load data from fmcpr.sm0.self.lh.nii.gz 
> with nibabel, and I get this error info:
>
 f.get_data()
> Traceback (most recent call last):
>File "", line 1, in 
>File "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line 341, in 
> get_data
>  return np.asanyarray(self._data)
>File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line 512, 
> in asanyarray
>  return array(a, dtype, copy=False, order=order, subok=True)
>File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 55, in 
> __array__
>  self._data = self._read_data()
>File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 60, in 
> _read_data
>  data = self.header.data_from_fileobj(fileobj)
>File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 486, in 
> data_from_fileobj
>  data = self.raw_data_from_fileobj(fileobj)
>File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 458, in 
> raw_data_from_fileobj
>  return array_from_file(shape, dtype, fileobj, offset)
>File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py", line 493, in 
> array_from_file
>  raise IOError(msg)
> IOError: Expected -1804 bytes, got 264809160 bytes from file 
> "fmcpr.vol2surf.lh.nii.gz"
>   - could the file be damaged?
>
> Then I check the file header by nibabel, and I get this:
>
 print(f.get_header())
>  object, endian='<'
> sizeof_hdr  : 348
> data_type   :
> db_name :
> extents : 0
> session_error   : 0
> regular :
> dim_info: 0
> dim : [  4  -1   1   1 451   1   1   1]
> intent_p1   : 0.0
> intent_p2   : 0.0
> intent_p3   : 0.0
> intent_code : none
> datatype: float32
> bitpix  : 32
> slice_start : 0
> pixdim  : [-1.  1.  1.  1.  
> 2.0072  1.  1.
>1.]
> vox_offset  : 352.0
> scl_slope   : 0.0
> scl_inter   : 0.0
> slice_end   : 0
> slice_code  : unknown
> xyzt_units  : 10
> cal_max : 0.0
> cal_min : 0.0
> slice_duration  : 0.0
> toffset : 0.0
> glmax   : 0
> glmin   : 146790
> descrip : FreeSurfer May 13 2013
> aux_file:
> qform_code  : scanner
> sform_code  : scanner
> quatern_b   : -0.0115927606821
> quatern_c   : -0.996071338654
> quatern_d   : -0.0864994972944
> qoffset_x   : 73344.5546875
> qoffset_y   : -1492.14978027
> qoffset_z   : -2311.28955078
> srow_x  : [ -9.99280393e-01   2.56918129e-02   2.79041883e-02   
> 7.33445547e+04]
> srow_y  : [  2.04970520e-02   9.84766901e-01  -1.72667429e-01  
> -1.49214978e+03]
> srow_z  : [  3.19152586e-02   1.71971247e-01   9.84584868e-01  
> -2.31128955e+03]
> intent_name :
> magic   : n+1
>
>
>
> Note that the dim has value -1, but when I use -surface fsaverage, the dim is 
> correct(show as below):
>
> dim : [4 27307 1 6   451 1 1 1]
>
> And I read the source code, the difference between self and fsaverage is 
> appeared when running rawfunc2surf-sess, and log files are attached.
>
> I have tried many 

Re: [Freesurfer] error with fcseed-config & fcseed-sess

[Douglas N Greve]

Those labels should exist in your individual subject's label folder. 
There should be a V1 label in there too. You can use mri_label2vol to 
create a binary volume in the anatomical space (this will be a volume 
where voxels values are either 1 (in V1) or 0 (out of V1)). This volume 
will be 256^3, 1mm3, and should go into the subject/mri folder (eg, 
lh.V1.mgz). When you run fcseed-config, specify -seg lh.V1.mgz -segid 1


On 07/27/2017 11:08 AM, Jessica Huang wrote:
> Hi Dr. Greeve,
>
> Would the following commands be enough to map my regions of interest 
> from the fsaverage map to my individual subjects?:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
>
> Namely, the following bits of code:
>
> cd $SUBJECTS_DIR
> mri_label2label \
>--srcsubject fsaverage \
>--srclabel fsaverage/label/lh.BA45.label \
>--trgsubject 004 \
>--trglabel 004/label/lh.BA45.label \
>--hemi lh \
>--regmethod surface
>
> On Thu, Jul 27, 2017 at 10:37 AM, Jessica Huang 
>  > wrote:
>
> Hi Dr. Greeve,
>
> Oh I see, thank you for the fix for V1. To probe further, I'm
> curious why the visual areas weren't implemented? Is there an
> additional step I could take to access other regions in the visual
> hierarchy such as V2, V3, and V5?
>
> Thanks for your insight Dr. Greeve,
> Jess
>
> On Jul 26, 2017 5:37 PM, "Douglas N Greve"
> > wrote:
>
> By default, you are using aparc+aseg.mgz as the ROI atlas, so
> use 1021
> or 2021 for V1.
>
> 1021ctx-lh-pericalcarine120 100 60  0
>
>
> On 07/26/2017 12:37 PM, Jessica Huang wrote:
> >
> > Hi freesurfer experts,
> >
> >
> > I’m using the fcseed-config and fcseed-sess commands to
> create a seed
> > at V1 in accordance with the FsFastFunctionalConnectivity
> Walkthrough
> >
> 
>  
> >Steps:
> >
> >
> > *STEP 4: Use fcseed-config to configure the parameters you
> wish to
> > pass to your connectivity analysis.Sample command: fcseed-config
> > -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean
> -cfg
> > mean.L_Posteriorcingulate.config*STEP 5: Create the FC seed
> for an
> > individualfcseed-sess  -s sessionid -cfg
> L_Posteriorcingulate.config
> >
> > V1 corresponds to the number 400 in
> > $FREESRUFER_HOME/FreeSurferColorLUT.txt. The subject session I’m
> > running is B101. The data is rest data but I named the file
> bold.
> > Overall, with this information specific to my data, I ran the
> > following commands:
> >
> >
> > INPUT
> >
> > $ fcseed-config -segid 400 -fcname V1.dat -fsd bold -mean -cfg
> > mean.V1.config
> >
> > OUTPUT
> >
> > fcname is V1.dat
> >
> > fcseed-config done
> >
> >
> > INPUT
> >
> > $ fcseed-sess  -s B101 -cfg mean.V1.config
> >
> > OUTPUT
> >
> > Logfile is
> >
> 
> /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/log/fcseed-sess.V1.dat.log.B101
> >
> > Wed Jul 26 12:27:17 EDT 2017
> >
> > Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version
> > 16.6.0: Fri Apr 14 16:21:16 PDT 2017;
> > root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64
> >
> > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects
> >
> > cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir
> >
> > /Applications/freesurfer/fsfast/bin/fcseed-sess
> >
> > -s B101 -cfg mean.V1.config
> >
> > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >
> > Wed Jul 26 12:27:17 EDT 2017
> >
> > Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version
> > 16.6.0: Fri Apr 14 16:21:16 PDT 2017;
> > root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64
> >
> > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects
> >
> > cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir
> >
> > /Applications/freesurfer/fsfast/bin/fcseed-sess
> >
> > -s B101 -cfg mean.V1.config
> >
> > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >
> >
> > mri_label2vol --seg
> >
> 
> /Users/caramazzalab/Desktop/Jess/Subjects/B201_mprage/mri/aparc+aseg.mgz
>  

Re: [Freesurfer] negative header after preproc-sess

[Douglas N Greve]

where are you getting those dims?


On 07/27/2017 09:24 AM, Bai Haohao wrote:
> Hi,
>
> Thanks for your reply. I tried mri_surf2surf --reshape or many other 
> methods but none of them could help.
>
> Then based on your explanation, I tried *mri_convert *.nii.gz *.mgz*, 
> and I could get data from mgz file, it really helps me, thank you!
>
> Besides, I am interested in the difference of dimension between 
> "-surface self"*(dim: -1 1 1)* and "-surface fsaverage"*(dim: 27307 1 
> 6)*, why does the dimension of "-surface fsaverage" be set like this 
> but "-surface self" do not? Is it possible to set the dimension of 
> "-surface self" during preprocessing to make sure every number is less 
> than 32k?
>
> Best,
>
> Bai Haohao
>
>
>
> On Thu, Jul 6, 2017 at 7:07 AM, Douglas Greve 
> > wrote:
>
> When the nifti standard was adopted, they used a short int to
> represent the dimensions. Unfortunately, this only allows for a
> maximum dimension of 32k, which is not big enough for surfaces. So
> I hacked the FS nifti format to put a -1 as the first dim at which
> point the FS code will go to another place in the header to get
> the spatial dimensions. It is possible to reshape the spatial
> dimensions as long as the largest prime factor is less than 32k
> (see mri_surf2surf with --reshape option). Other than that, you
> might ask the nibabel people to program the same hack.
>
>
> On 6/25/17 6:48 AM, Bai Haohao wrote:
>> Hello Freesurfer experts,
>>
>> I am running my data with preproc-sess to project my func data to
>> individual anatomy file, and the command shows as below:
>>
>> preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh
>> -fwhm 0 -per-run -force
>>
>>
>> And the subjectname point to the subject dir that created after
>> recon-all.
>>
>> After the running completed, I try to load data from
>> fmcpr.sm0.self.lh.nii.gz with nibabel, and I get this error info:
>>
>> >>> f.get_data()
>> Traceback (most recent call last):
>>   File "", line 1, in 
>>   File
>> "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line
>> 341, in get_data
>> return np.asanyarray(self._data)
>>   File
>> "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py",
>> line 512, in asanyarray
>> return array(a, dtype, copy=False, order=order, subok=True)
>>   File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py",
>> line 55, in __array__
>> self._data = self._read_data()
>>   File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py",
>> line 60, in _read_data
>> data = self.header.data_from_fileobj(fileobj)
>>   File "/usr/lib/pymodules/python2.7/nibabel/analyze.py",
>> line 486, in data_from_fileobj
>> data = self.raw_data_from_fileobj(fileobj)
>>   File "/usr/lib/pymodules/python2.7/nibabel/analyze.py",
>> line 458, in raw_data_from_fileobj
>> return array_from_file(shape, dtype, fileobj, offset)
>>   File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py",
>> line 493, in array_from_file
>> raise IOError(msg)
>> IOError: Expected -1804 bytes, got 264809160 bytes from file
>> "fmcpr.vol2surf.lh.nii.gz"
>>  - could the file be damaged?
>>
>>
>> Then I check the file header by nibabel, and I get this:
>>
>>
>> >>> print(f.get_header())
>>  object, endian='<'
>> sizeof_hdr  : 348
>> data_type :
>> db_name :
>> extents : 0
>> session_error : 0
>> regular :
>> dim_info  : 0
>> dim : [  4  -1   1   1 451   1   1   1]
>> intent_p1 : 0.0
>> intent_p2 : 0.0
>> intent_p3 : 0.0
>> intent_code : none
>> datatype  : float32
>> bitpix  : 32
>> slice_start : 0
>> pixdim  : [-1.  1.  1.1.
>>  2.0072  1.  1.
>>   1.]
>> vox_offset  : 352.0
>> scl_slope : 0.0
>> scl_inter : 0.0
>> slice_end : 0
>> slice_code  : unknown
>> xyzt_units  : 10
>> cal_max : 0.0
>> cal_min : 0.0
>> slice_duration  : 0.0
>> toffset : 0.0
>> glmax : 0
>> glmin : 146790
>> descrip : FreeSurfer May 13 2013
>> aux_file  :
>> qform_code  : scanner
>> sform_code  : scanner
>> quatern_b : -0.0115927606821
>> quatern_c : -0.996071338654
>> quatern_d : -0.0864994972944
>> qoffset_x : 73344.5546875
>> qoffset_y : -1492.14978027
>> qoffset_z : -2311.28955078
>> srow_x  : [ -9.99280393e-01   2.56918129e-02   2.79041883e-02
>>   7.33445547e+04]
>> srow_y  : [  

Re: [Freesurfer] extract values for significant cluster

[Douglas N Greve]

You can use mri_segstats specifying the ocn as the segmentation, the 
stack of thicknesses as the input, and --avgwf file.dat as the output. 
Make sure to add --excludeid 0 to exclude background voxels


On 07/27/2017 06:18 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> in the longitudinal 2 stage model I find a difference in rate between my two 
> groups in right intra parietal sulcus for surface area (survives MC 
> correction). I would like to look at the cortical thickness in that same 
> cluster. Is it possible to use any of the output files from the MC correction 
> as a mask or something to get the rate of change values for thickness in that 
> region? Even though this region does not show a significant difference 
> between the groups I would like to look at the individual values for rate of 
> change in that specific region (like the ones I received in the 
> cache.th30.abs.y.ocn.dat file)
>
> Could you please tell me if this is possible and how?
>
> Thank you very much!
> Clara
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] Pial surface missing GM

[Bruce Fischl]

Hi Jake

there are voxels like 173, 112, 122 that are incorrectly segmented as wm 
(that is, they have a value >=5 in the wm.mgz) that connect two adjenct 
gyri. You can either change the intensity thresholds in mri_segment, or 
manually erase some of them. The best way to see this is to look at the 
surface prior to topology correction, and color it with defect numbers so 
you can see where the defects are. Something like:


cd $SUBJECTS_DIR//mri
freeview -v brain.mgz wm.mgz:colormap=heat:heatscale=1,100 \
-f 
../surf/lh.orig.nofix:overlay=../surf/lh.defect_labels:overlay_threshold=1,255:edgecolor=overlay
 \
-slice 172 123 134


if you page through a few axial slices you will see that the wm.mgz is 
connected to the body of the wm in slice 109, disconnecs in 110, then 
reconnects to a different part in 115, which should never happen


cheers
Bruce
 On Thu, 27 
Jul 2017, Jake Rieke wrote:



Hi Bruce,

Thanks for the response. I just uploaded the subject using the ftp file
exchange. The issue is visible in the region close to voxel coordinate [172,
123 ,134]. the missing gyrus is capped between coronal slice 141 to 118. I
forgot to mention in my first message that we used a T2 to improve pial
surface after initial running with just the T1.

Thanks again
Jake

Biomedical Engineer, Brain Rehabilitation Research CenterMalcolm Randall VA
Medical Center, 1601 SW Archer Road, Gainesville, FL 32608
Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com

On Wed, Jul 26, 2017 at 8:16 PM, Bruce Fischl 
wrote:
  Hi Jake

  usually that means that there is a topology defect that is being
  incorrectly fixed. If you upload the subject and point us at the
  voxel
  coords we will take a look

  cheers
  Bruce

  On Wed, 26 Jul 2017, Jake Rieke wrote:

  > Hello surfers,
  >
  > I'm attempting to extend white and pial surfaces to encompass
  an
  > unrecognized gyrus. The wm.mgz seems include the WM tissue,
  but the white
  > surface does not extend to the WM boundary. I thought this
  might be related
  > to an intensity normalization error and tried using control
  points, but that
  > did not make a big difference in the resulting surfaces. I've
  attached
  > pictures to better illustrate the problem. Thanks in advance
  for your help!
  >
  > Best regards,
  > Jake
  >
  >
  >
___
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


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] Extract coordinates from .mgh file

[Douglas N Greve]

Use mri_annotation2label to create a label, which will have 
tkregisterRAS coordinates


On 07/26/2017 08:32 PM, Md. Mamun Al-Amin wrote:
> Hi
> I would like to extract cooridantes of "aparc.a2009s+aseg.mgz" file. 
> This file is stored in the mri folder.
> Would you please help me in this regards?
>
> kind regards
> Mamun
>
> On Thu, Jul 27, 2017 at 9:36 AM, Redwan Maatoug 
> > wrote:
>
> Hi Doug,
>
> Thank you for your reply,
> I have used the tool *surf_cluster* to have the MNI coordinates.
> Is it a good alternative to *mri_cor2label *?
>
> Thank you very much,
> Regards,
> Redwan
>
> On Wed, Jul 26, 2017 at 2:41 PM, Douglas N Greve
> > wrote:
>
> mri_cor2label with extract the coordinates into a label file. The
> coordinates will be in "tkregisterRAS". What coordinate system
> do you
> want? See
>
> See
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> 
>
>
> On 07/25/2017 07:32 PM, Redwan Maatoug wrote:
> > Hi experts,
> >
> > I just want to know a way to extract the coordinates from a
> ROI mgh file.
> >
> > I know that I can load the file with tksurfer but I have 100
> .mgh
> > files so if I could run a command line to have the
> coordinates in a
> > .txt file or in a .m it would be helpful.
> >
> > Thank you,
> > Redwan
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
>
> ___
> 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
> 
>
>
> 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.
>
>
>
>
> -- 
>
> Kind regards
>
> Md. Mamun Al-Amin
> --
> PhD Candidate, Queensland Brain Institute
> Building 79, St Lucia QLD 4072
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: 

Re: [Freesurfer] Pial surface missing GM

[Douglas N Greve]

you can also run defect-seg, then look at the help to get an idea of how 
to load the defect segmentation and see whether the defect is causing 
the problem


On 07/26/2017 08:16 PM, Bruce Fischl wrote:
> Hi Jake
>
> usually that means that there is a topology defect that is being
> incorrectly fixed. If you upload the subject and point us at the voxel
> coords we will take a look
>
> cheers
> Bruce
>
> On Wed, 26 Jul 2017, Jake Rieke wrote:
>
>> Hello surfers,
>>
>> I'm attempting to extend white and pial surfaces to encompass an
>> unrecognized gyrus. The wm.mgz seems include the WM tissue, but the white
>> surface does not extend to the WM boundary. I thought this might be related
>> to an intensity normalization error and tried using control points, but that
>> did not make a big difference in the resulting surfaces. I've attached
>> pictures to better illustrate the problem. Thanks in advance for your help!
>>
>> Best regards,
>> Jake
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] Extract coordinates from .mgh file

[Douglas N Greve]

yea, that works too


On 07/26/2017 07:36 PM, Redwan Maatoug wrote:
> Hi Doug,
>
> Thank you for your reply,
> I have used the tool *surf_cluster* to have the MNI coordinates.
> Is it a good alternative to *mri_cor2label *?
>
> Thank you very much,
> Regards,
> Redwan
>
> On Wed, Jul 26, 2017 at 2:41 PM, Douglas N Greve 
> > wrote:
>
> mri_cor2label with extract the coordinates into a label file. The
> coordinates will be in "tkregisterRAS". What coordinate system do you
> want? See
>
> See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> 
>
>
> On 07/25/2017 07:32 PM, Redwan Maatoug wrote:
> > Hi experts,
> >
> > I just want to know a way to extract the coordinates from a ROI
> mgh file.
> >
> > I know that I can load the file with tksurfer but I have 100 .mgh
> > files so if I could run a command line to have the coordinates in a
> > .txt file or in a .m it would be helpful.
> >
> > Thank you,
> > Redwan
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
>
> ___
> 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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

Re: [Freesurfer] mri_glmfit --cortex flag

[Douglas N Greve]

right, that should not be happening


On 07/27/2017 12:39 PM, Rockers, Elijah D. wrote:
> From what I understand, the --cortex flag is simply supposed to zero 
> out any signal in the medial wall with a mask, I checked mask.mgh, it 
> is 0 on the medial wall and 1 everywhere else as expected... however 
> when I analyze the data without this flag, the resulting sig.mgh file 
> has completely changed. Areas on the cortex that were "lit up" 
> disappear, and other areas light up that were silent before. This 
> should not be happening right?
>
> Houston Methodist. Leading Medicine.
>
> /U.S. News & World Report/ has recognized Houston Methodist as one of 
> the nation’s top 20 hospitals, placing it for the second time on the 
> magazine’s prestigious Honor Roll. It is also designated as a Magnet 
> hospital for excellence in nursing. Visit us at houstonmethodist.org 
> . Follow us at twitter.com/MethodistHosp 
>  and facebook.com/HoustonMethodist.
>
> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston 
> Methodist and/or its relevant affiliates and may contain restricted 
> and privileged material for the sole use of the intended recipient(s). 
> Any review, use, distribution or disclosure by others is strictly 
> prohibited. If you are not the intended recipient (or authorized to 
> receive for the recipient), please contact the sender and delete all 
> copies of the message. Thank you.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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] mri_glmfit --cortex flag

[Rockers, Elijah D.]

From what I understand, the --cortex flag is simply supposed to zero out any 
signal in the medial wall with a mask, I checked mask.mgh, it is 0 on the 
medial wall and 1 everywhere else as expected... however when I analyze the 
data without this flag, the resulting sig.mgh file has completely changed. 
Areas on the cortex that were "lit up" disappear, and other areas light up that 
were silent before. This should not be happening right?

Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
Houston Methodist as one of the nation’s top 20 hospitals, placing it for the 
second time on the magazine’s prestigious Honor Roll. It is also designated as 
a Magnet hospital for excellence in nursing.  Visit us at  
houstonmethodist.org. Follow us at  twitter.com/MethodistHosp and 
facebook.com/HoustonMethodist.  ***CONFIDENTIALITY NOTICE*** This e-mail is the 
property of Houston Methodist and/or its relevant affiliates and may contain 
restricted and privileged material for the sole use of the intended 
recipient(s). Any review, use, distribution or disclosure by others is strictly 
prohibited. If you are not the intended recipient (or authorized to receive for 
the recipient), please contact the sender and delete all copies of the message. 
Thank you.
___
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.

Re: [Freesurfer] negative header after preproc-sess

[Christopher Markiewicz]

Hi Doug,

I wonder if there's a plan to move to NIfTI-2 as the default encoding for 
.nii(.gz) images that would can't be encoded in a standard-conforming NIfTI-1? 
I believe all of the major packages support NIfTI-2 in their latest releases 
(with the possible exception of ANTs, which I don't believe handles surface 
data in any event).

Chris Markiewwicz

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

Sent: Wednesday, July 5, 2017 7:07:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] negative header after preproc-sess

When the nifti standard was adopted, they used a short int to represent the 
dimensions. Unfortunately, this only allows for a maximum dimension of 32k, 
which is not big enough for surfaces. So I hacked the FS nifti format to put a 
-1 as the first dim at which point the FS code will go to another place in the 
header to get the spatial dimensions. It is possible to reshape the spatial 
dimensions as long as the largest prime factor is less than 32k (see 
mri_surf2surf with --reshape option). Other than that, you might ask the 
nibabel people to program the same hack.

On 6/25/17 6:48 AM, Bai Haohao wrote:
Hello Freesurfer experts,

I am running my data with preproc-sess to project my func data to individual 
anatomy file, and the command shows as below:

preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh -fwhm 0 -per-run 
-force

And the subjectname point to the subject dir that created after recon-all.

After the running completed, I try to load data from fmcpr.sm0.self.lh.nii.gz 
with nibabel, and I get this error info:

>>> f.get_data()
Traceback (most recent call last):
  File "", line 1, in 
  File "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line 341, in 
get_data
return np.asanyarray(self._data)
  File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line 512, in 
asanyarray
return array(a, dtype, copy=False, order=order, subok=True)
  File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 55, in 
__array__
self._data = self._read_data()
  File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 60, in 
_read_data
data = self.header.data_from_fileobj(fileobj)
  File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 486, in 
data_from_fileobj
data = self.raw_data_from_fileobj(fileobj)
  File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 458, in 
raw_data_from_fileobj
return array_from_file(shape, dtype, fileobj, offset)
  File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py", line 493, in 
array_from_file
raise IOError(msg)
IOError: Expected -1804 bytes, got 264809160 bytes from file 
"fmcpr.vol2surf.lh.nii.gz"
 - could the file be damaged?

Then I check the file header by nibabel, and I get this:

>>> print(f.get_header())
 object, endian='<'
sizeof_hdr  : 348
data_type   :
db_name :
extents : 0
session_error   : 0
regular :
dim_info: 0
dim : [  4  -1   1   1 451   1   1   1]
intent_p1   : 0.0
intent_p2   : 0.0
intent_p3   : 0.0
intent_code : none
datatype: float32
bitpix  : 32
slice_start : 0
pixdim  : [-1.  1.  1.  1.  2.0072  
1.  1.
  1.]
vox_offset  : 352.0
scl_slope   : 0.0
scl_inter   : 0.0
slice_end   : 0
slice_code  : unknown
xyzt_units  : 10
cal_max : 0.0
cal_min : 0.0
slice_duration  : 0.0
toffset : 0.0
glmax   : 0
glmin   : 146790
descrip : FreeSurfer May 13 2013
aux_file:
qform_code  : scanner
sform_code  : scanner
quatern_b   : -0.0115927606821
quatern_c   : -0.996071338654
quatern_d   : -0.0864994972944
qoffset_x   : 73344.5546875
qoffset_y   : -1492.14978027
qoffset_z   : -2311.28955078
srow_x  : [ -9.99280393e-01   2.56918129e-02   2.79041883e-02   
7.33445547e+04]
srow_y  : [  2.04970520e-02   9.84766901e-01  -1.72667429e-01  
-1.49214978e+03]
srow_z  : [  3.19152586e-02   1.71971247e-01   9.84584868e-01  
-2.31128955e+03]
intent_name :
magic   : n+1



Note that the dim has value -1, but when I use -surface fsaverage, the dim is 
correct(show as below):

dim : [4 27307 1 6   451 1 1 1]

And I read the source code, the difference between self and fsaverage is 
appeared when running rawfunc2surf-sess, and log files are attached.

I have tried many commands to load data from fmcpr.sm0.self.lh.nii.gz, such as 
fslview, freeview, mri_convert, mri_surf2surf, ...

and only tksurfer could read this file by -timecourse fmcpr.sm0.self.lh.nii.gz.

I want to figure out how could I fix it, and any suggestion would be helpful.

Thanks in advance,

Bai Haohao


Version info:
System: 

Re: [Freesurfer] error with fcseed-config & fcseed-sess

[Jessica Huang]

Hi Dr. Greeve,

Would the following commands be enough to map my regions of interest from
the fsaverage map to my individual subjects?:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

Namely, the following bits of code:

cd $SUBJECTS_DIR
mri_label2label \
  --srcsubject fsaverage \
  --srclabel fsaverage/label/lh.BA45.label \
  --trgsubject 004 \
  --trglabel 004/label/lh.BA45.label \
  --hemi lh \
  --regmethod surface


On Thu, Jul 27, 2017 at 10:37 AM, Jessica Huang <
jessica_hu...@college.harvard.edu> wrote:

> Hi Dr. Greeve,
>
> Oh I see, thank you for the fix for V1. To probe further, I'm curious why
> the visual areas weren't implemented? Is there an additional step I could
> take to access other regions in the visual hierarchy such as V2, V3, and V5?
>
> Thanks for your insight Dr. Greeve,
> Jess
>
> On Jul 26, 2017 5:37 PM, "Douglas N Greve" 
> wrote:
>
>> By default, you are using aparc+aseg.mgz as the ROI atlas, so use 1021
>> or 2021 for V1.
>>
>> 1021ctx-lh-pericalcarine120 100 60  0
>>
>>
>> On 07/26/2017 12:37 PM, Jessica Huang wrote:
>> >
>> > Hi freesurfer experts,
>> >
>> >
>> > I’m using the fcseed-config and fcseed-sess commands to create a seed
>> > at V1 in accordance with the FsFastFunctionalConnectivity Walkthrough
>> > > nnectivityWalkthrough>Steps:
>> >
>> >
>> > *STEP 4: Use fcseed-config to configure the parameters you wish to
>> > pass to your connectivity analysis.Sample command: fcseed-config
>> > -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg
>> > mean.L_Posteriorcingulate.config*STEP 5: Create the FC seed for an
>> > individualfcseed-sess  -s sessionid -cfg L_Posteriorcingulate.config
>> >
>> > V1 corresponds to the number 400 in
>> > $FREESRUFER_HOME/FreeSurferColorLUT.txt. The subject session I’m
>> > running is B101. The data is rest data but I named the file bold.
>> > Overall, with this information specific to my data, I ran the
>> > following commands:
>> >
>> >
>> > INPUT
>> >
>> > $ fcseed-config -segid 400 -fcname V1.dat -fsd bold -mean -cfg
>> > mean.V1.config
>> >
>> > OUTPUT
>> >
>> > fcname is V1.dat
>> >
>> > fcseed-config done
>> >
>> >
>> > INPUT
>> >
>> > $ fcseed-sess  -s B101 -cfg mean.V1.config
>> >
>> > OUTPUT
>> >
>> > Logfile is
>> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/log/
>> fcseed-sess.V1.dat.log.B101
>> >
>> > Wed Jul 26 12:27:17 EDT 2017
>> >
>> > Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version
>> > 16.6.0: Fri Apr 14 16:21:16 PDT 2017;
>> > root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64
>> >
>> > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects
>> >
>> > cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir
>> >
>> > /Applications/freesurfer/fsfast/bin/fcseed-sess
>> >
>> > -s B101 -cfg mean.V1.config
>> >
>> > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>> >
>> > Wed Jul 26 12:27:17 EDT 2017
>> >
>> > Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version
>> > 16.6.0: Fri Apr 14 16:21:16 PDT 2017;
>> > root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64
>> >
>> > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects
>> >
>> > cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir
>> >
>> > /Applications/freesurfer/fsfast/bin/fcseed-sess
>> >
>> > -s B101 -cfg mean.V1.config
>> >
>> > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>> >
>> >
>> > mri_label2vol --seg
>> > /Users/caramazzalab/Desktop/Jess/Subjects/B201_mprage/mri/ap
>> arc+aseg.mgz
>> > --reg
>> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101
>> /bold/001/register.dof6.lta
>> > --temp
>> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101
>> /bold/001/template.nii.gz
>> > --fillthresh .5 --o
>> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101
>> /bold/001/tmp.fcseed-sess.47801/seg.nii.gz
>> > --pvf
>> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101
>> /bold/001/tmp.fcseed-sess.47801/pvf.nii.gz
>> >
>> > PVF
>> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101
>> /bold/001/tmp.fcseed-sess.47801/pvf.nii.gz
>> >
>> > Number of labels: 0
>> >
>> > Annot File:  (null)
>> >
>> > Template Volume:
>> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101
>> /bold/001/template.nii.gz
>> >
>> > Outut Volume:
>> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101
>> /bold/001/tmp.fcseed-sess.47801/seg.nii.gz
>> >
>> > Registration File:
>> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101
>> /bold/001/register.dof6.lta
>> >
>> > Fill Threshold: 0.5
>> >
>> > Label Vox Vol:  1
>> >
>> > ProjType:   (null)
>> >
>> > ProjTypeId: 0
>> >
>> > ProjStart:  0
>> >
>> > ProjStop:   0
>> >
>> > ProjDelta:  0.1
>> >
>> > Subject:  (null)
>> >
>> > Hemi: (null)
>> >
>> > UseNewASeg2Vol:  0
>> >
>> > DoLabelStatVol  0
>> >
>> > LabelCodeOffset  0
>> >
>> > setenv 

Re: [Freesurfer] error with fcseed-config & fcseed-sess

[Jessica Huang]

Hi Dr. Greeve,

Oh I see, thank you for the fix for V1. To probe further, I'm curious why
the visual areas weren't implemented? Is there an additional step I could
take to access other regions in the visual hierarchy such as V2, V3, and V5?

Thanks for your insight Dr. Greeve,
Jess

On Jul 26, 2017 5:37 PM, "Douglas N Greve" 
wrote:

> By default, you are using aparc+aseg.mgz as the ROI atlas, so use 1021
> or 2021 for V1.
>
> 1021ctx-lh-pericalcarine120 100 60  0
>
>
> On 07/26/2017 12:37 PM, Jessica Huang wrote:
> >
> > Hi freesurfer experts,
> >
> >
> > I’m using the fcseed-config and fcseed-sess commands to create a seed
> > at V1 in accordance with the FsFastFunctionalConnectivity Walkthrough
> >  lkthrough>Steps:
> >
> >
> > *STEP 4: Use fcseed-config to configure the parameters you wish to
> > pass to your connectivity analysis.Sample command: fcseed-config
> > -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg
> > mean.L_Posteriorcingulate.config*STEP 5: Create the FC seed for an
> > individualfcseed-sess  -s sessionid -cfg L_Posteriorcingulate.config
> >
> > V1 corresponds to the number 400 in
> > $FREESRUFER_HOME/FreeSurferColorLUT.txt. The subject session I’m
> > running is B101. The data is rest data but I named the file bold.
> > Overall, with this information specific to my data, I ran the
> > following commands:
> >
> >
> > INPUT
> >
> > $ fcseed-config -segid 400 -fcname V1.dat -fsd bold -mean -cfg
> > mean.V1.config
> >
> > OUTPUT
> >
> > fcname is V1.dat
> >
> > fcseed-config done
> >
> >
> > INPUT
> >
> > $ fcseed-sess  -s B101 -cfg mean.V1.config
> >
> > OUTPUT
> >
> > Logfile is
> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/
> log/fcseed-sess.V1.dat.log.B101
> >
> > Wed Jul 26 12:27:17 EDT 2017
> >
> > Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version
> > 16.6.0: Fri Apr 14 16:21:16 PDT 2017;
> > root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64
> >
> > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects
> >
> > cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir
> >
> > /Applications/freesurfer/fsfast/bin/fcseed-sess
> >
> > -s B101 -cfg mean.V1.config
> >
> > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >
> > Wed Jul 26 12:27:17 EDT 2017
> >
> > Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version
> > 16.6.0: Fri Apr 14 16:21:16 PDT 2017;
> > root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64
> >
> > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects
> >
> > cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir
> >
> > /Applications/freesurfer/fsfast/bin/fcseed-sess
> >
> > -s B101 -cfg mean.V1.config
> >
> > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >
> >
> > mri_label2vol --seg
> > /Users/caramazzalab/Desktop/Jess/Subjects/B201_mprage/mri/aparc+aseg.mgz
> > --reg
> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/
> B101/bold/001/register.dof6.lta
> > --temp
> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/
> B101/bold/001/template.nii.gz
> > --fillthresh .5 --o
> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/
> B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz
> > --pvf
> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/
> B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz
> >
> > PVF
> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/
> B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz
> >
> > Number of labels: 0
> >
> > Annot File:  (null)
> >
> > Template Volume:
> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/
> B101/bold/001/template.nii.gz
> >
> > Outut Volume:
> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/
> B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz
> >
> > Registration File:
> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/
> B101/bold/001/register.dof6.lta
> >
> > Fill Threshold: 0.5
> >
> > Label Vox Vol:  1
> >
> > ProjType:   (null)
> >
> > ProjTypeId: 0
> >
> > ProjStart:  0
> >
> > ProjStop:   0
> >
> > ProjDelta:  0.1
> >
> > Subject:  (null)
> >
> > Hemi: (null)
> >
> > UseNewASeg2Vol:  0
> >
> > DoLabelStatVol  0
> >
> > LabelCodeOffset  0
> >
> > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects
> >
> > $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
> >
> > Template RAS-to-Vox: 
> >
> > -0.5  -0.0  -0.0   56.0;
> >
> > -0.0  -0.0  -0.5   56.0;
> >
> > -0.0   0.45455  -0.0   32.0;
> >
> > -0.0  -0.0  -0.0   1.0;
> >
> > Template Voxel Volume: 8.8
> >
> > nHits Thresh: 4.4
> >
> > Loading registration from
> > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/
> B101/bold/001/register.dof6.lta
> >
> > regio_read_register: loading lta
> >
> > RegMat: 
> >
> > 0.99785   0.02664   0.05987   0.19449;
> >
> > -0.06077   0.03415   0.99757  -39.76084;

Re: [Freesurfer] negative header after preproc-sess

[Bai Haohao]

Hi,

Thanks for your reply. I tried mri_surf2surf --reshape or many other
methods but none of them could help.

Then based on your explanation, I tried *mri_convert *.nii.gz *.mgz*, and I
could get data from mgz file, it really helps me, thank you!

Besides, I am interested in the difference of dimension between "-surface
self"*(dim: -1 1 1)* and "-surface fsaverage"*(dim: 27307 1 6)*, why does
the dimension of "-surface fsaverage" be set like this but "-surface self"
do not? Is it possible to set the dimension of "-surface self" during
preprocessing to make sure every number is less than 32k?

Best,

Bai Haohao



On Thu, Jul 6, 2017 at 7:07 AM, Douglas Greve 
wrote:

> When the nifti standard was adopted, they used a short int to represent
> the dimensions. Unfortunately, this only allows for a maximum dimension of
> 32k, which is not big enough for surfaces. So I hacked the FS nifti format
> to put a -1 as the first dim at which point the FS code will go to another
> place in the header to get the spatial dimensions. It is possible to
> reshape the spatial dimensions as long as the largest prime factor is less
> than 32k (see mri_surf2surf with --reshape option). Other than that, you
> might ask the nibabel people to program the same hack.
>
> On 6/25/17 6:48 AM, Bai Haohao wrote:
>
> Hello Freesurfer experts,
>
> I am running my data with preproc-sess to project my func data to
> individual anatomy file, and the command shows as below:
>
> preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh -fwhm 0
> -per-run -force
>
>
> And the subjectname point to the subject dir that created after recon-all.
>
> After the running completed, I try to load data from
> fmcpr.sm0.self.lh.nii.gz with nibabel, and I get this error info:
>
> >>> f.get_data()
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line 341,
> in get_data
> return np.asanyarray(self._data)
>   File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line
> 512, in asanyarray
> return array(a, dtype, copy=False, order=order, subok=True)
>   File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 55, in
> __array__
> self._data = self._read_data()
>   File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 60, in
> _read_data
> data = self.header.data_from_fileobj(fileobj)
>   File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 486, in
> data_from_fileobj
> data = self.raw_data_from_fileobj(fileobj)
>   File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 458, in
> raw_data_from_fileobj
> return array_from_file(shape, dtype, fileobj, offset)
>   File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py", line 493,
> in array_from_file
> raise IOError(msg)
> IOError: Expected -1804 bytes, got 264809160 bytes from file
> "fmcpr.vol2surf.lh.nii.gz"
>  - could the file be damaged?
>
>
> Then I check the file header by nibabel, and I get this:
>
>
> >>> print(f.get_header())
>  object, endian='<'
> sizeof_hdr  : 348
> data_type   :
> db_name :
> extents : 0
> session_error   : 0
> regular :
> dim_info: 0
> dim : [  4  -1   1   1 451   1   1   1]
> intent_p1   : 0.0
> intent_p2   : 0.0
> intent_p3   : 0.0
> intent_code : none
> datatype: float32
> bitpix  : 32
> slice_start : 0
> pixdim  : [-1.  1.  1.  1.
>  2.0072  1.  1.
>   1.]
> vox_offset  : 352.0
> scl_slope   : 0.0
> scl_inter   : 0.0
> slice_end   : 0
> slice_code  : unknown
> xyzt_units  : 10
> cal_max : 0.0
> cal_min : 0.0
> slice_duration  : 0.0
> toffset : 0.0
> glmax   : 0
> glmin   : 146790
> descrip : FreeSurfer May 13 2013
> aux_file:
> qform_code  : scanner
> sform_code  : scanner
> quatern_b   : -0.0115927606821
> quatern_c   : -0.996071338654
> quatern_d   : -0.0864994972944
> qoffset_x   : 73344.5546875
> qoffset_y   : -1492.14978027
> qoffset_z   : -2311.28955078
> srow_x  : [ -9.99280393e-01   2.56918129e-02   2.79041883e-02
> 7.33445547e+04]
> srow_y  : [  2.04970520e-02   9.84766901e-01  -1.72667429e-01
>  -1.49214978e+03]
> srow_z  : [  3.19152586e-02   1.71971247e-01   9.84584868e-01
>  -2.31128955e+03]
> intent_name :
> magic   : n+1
>
>
>
>
> Note that the dim has value -1, but when I use -surface fsaverage, the dim
> is correct(show as below):
>
> dim : [4 27307 1 6   451 1 1 1]
>
>
> And I read the source code, the difference between self and fsaverage is
> appeared when running rawfunc2surf-sess, and log files are attached.
>
> I have tried many commands to load data from fmcpr.sm0.self.lh.nii.gz,
> such as fslview, freeview, mri_convert, mri_surf2surf, ...
>
> and only 

Re: [Freesurfer] Pial surface missing GM

[Jake Rieke]

Hi Bruce,

Thanks for the response. I just uploaded the subject using the ftp file
exchange. The issue is visible in the region close to voxel coordinate
[172, 123 ,134]. the missing gyrus is capped between coronal slice 141 to
118. I forgot to mention in my first message that we used a T2 to improve
pial surface after initial running with just the T1.

Thanks again
Jake

Biomedical Engineer, Brain Rehabilitation Research Center
Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL
32608
Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com

On Wed, Jul 26, 2017 at 8:16 PM, Bruce Fischl 
wrote:

> Hi Jake
>
> usually that means that there is a topology defect that is being
> incorrectly fixed. If you upload the subject and point us at the voxel
> coords we will take a look
>
> cheers
> Bruce
>
> On Wed, 26 Jul 2017, Jake Rieke wrote:
>
> > Hello surfers,
> >
> > I'm attempting to extend white and pial surfaces to encompass an
> > unrecognized gyrus. The wm.mgz seems include the WM tissue, but the white
> > surface does not extend to the WM boundary. I thought this might be
> related
> > to an intensity normalization error and tried using control points, but
> that
> > did not make a big difference in the resulting surfaces. I've attached
> > pictures to better illustrate the problem. Thanks in advance for your
> help!
> >
> > Best regards,
> > Jake
> >
> >
> >
> ___
> 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


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] extract values for significant cluster

[Clara Kühn]

Dear FreeSurfer experts,

in the longitudinal 2 stage model I find a difference in rate between my two 
groups in right intra parietal sulcus for surface area (survives MC 
correction). I would like to look at the cortical thickness in that same 
cluster. Is it possible to use any of the output files from the MC correction 
as a mask or something to get the rate of change values for thickness in that 
region? Even though this region does not show a significant difference between 
the groups I would like to look at the individual values for rate of change in 
that specific region (like the ones I received in the cache.th30.abs.y.ocn.dat 
file)

Could you please tell me if this is possible and how?

Thank you very much!
Clara

-- 
Clara Kühn, Phd Candidate
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

___
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] recon-all error: ERROR! FOV=272.000 > 256

[juhyoung Ryu]

Hi experts,


I'm trying to surface reconstruction using high-resolution T1 and T2 data
using freesurfer version 6
So I typed like this:
recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial
-all


and that excited with errors like this;

\n

ERROR! FOV=272.000 > 256

Include the flag -cw256 with recon-all!

Inspect orig.mgz to ensure the head is fully visible.

\n


So I added -cw256 flag and run the command line again (recon-all -subject
${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all -cw256). But
the result is same.



I'd appreciate any suggestion.


Thank you,

Juhyoung
___
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.