Re: [Freesurfer] recon-all exits with errors

[Ali Radaideh]

Dear Bruce,

many thanks for your email. I have noticed that the FreeSurfer I am still
using is 5.3.0 and this version seems not to work with my Ubuntu 16.10 due
to issues related to the current version of "Perl" (version 22).  I have
just downloaded the latest version of FreeSurfer (version 6) and everything
seems to work fine.

Many thanks,
Ali

On Fri, Oct 6, 2017 at 4:24 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Ali
>
> can you send us your full command line, the full screen output and the
> recon-all.log file that should have been generated in the subject's scripts
> dir?
>
> cheers
> Bruce
> On Fri, 6 Oct 2017, Ali Radaideh wrote:
>
> Dear FreeSurfer Experts,
>>
>> I have just launched a new project and collected new T1 weighted images
>> (as my previous ones) and
>> started processing them using FreeSurfer. Unfortunaely non of them works
>> with FreeSurfer. When I run
>> recon-all -autorecon-all -s subjecname, I get the following error:
>>
>> #@# Talairach Fri Oct  6 09:20:02 EEST 2017
>> /home/ali/processing/Farah_hospital/MR.BASHEER_IGIAM/mcropped_noor/mri
>>
>>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>> --i orig.mgz --o
>> orig_nu.mgz
>>
>> Linux ali-XPS-L501X 4.8.0-54-generic #57-Ubuntu SMP Wed May 24 10:21:44
>> UTC 2017 x86_64 x86_64
>> x86_64 GNU/Linux
>>
>> recon-all -s mcropped_noor exited with ERRORS at Fri Oct  6 09:20:05 EEST
>> 2017
>>
>> To report a problem, see http://surfer.nmr.mgh.harvard.
>> edu/fswiki/BugReporting
>>
>>
>>
>> I have checked my images and they look fine and they are similar to the
>> ones I have processed a year
>> ago.
>>
>> I have searched for a solution to this error but unfortunately I did not
>> find any. Could you please
>> help me on this?
>>
>> Thanks alot in advance,
>>
>> Ali
>>
>> --
>> Ali M. Al-Radaideh. PhD
>> Department of Medical Imaging
>> Faculty of Allied Health Sciences
>> The Hashemite University,
>> Zarqa, Jordan
>> W.phone +962 5 390 ext.5422, 5355, 5364
>> Email: ali.radai...@hu.edu.jo
>> webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
>>
>>
>>
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-- 







*Ali M. Al-Radaideh. PhDDepartment of Medical ImagingFaculty of Allied
Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5
390 ext.5422, 5355, 5364Email: ali.radai...@hu.edu.jo
<ali.radai...@hu.edu.jo>*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
<http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*
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[Freesurfer] recon-all exits with errors

[Ali Radaideh]

Dear FreeSurfer Experts,

I have just launched a new project and collected new T1 weighted images (as
my previous ones) and started processing them using FreeSurfer.
Unfortunaely non of them works with FreeSurfer. When I run recon-all
-autorecon-all -s subjecname, I get the following error:

#@# Talairach Fri Oct  6 09:20:02 EEST 2017
/home/ali/processing/Farah_hospital/MR.BASHEER_IGIAM/mcropped_noor/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz

Linux ali-XPS-L501X 4.8.0-54-generic #57-Ubuntu SMP Wed May 24 10:21:44 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s mcropped_noor exited with ERRORS at Fri Oct  6 09:20:05 EEST
2017

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



I have checked my images and they look fine and they are similar to the
ones I have processed a year ago.

I have searched for a solution to this error but unfortunately I did not
find any. Could you please help me on this?

Thanks alot in advance,

Ali

-- 







*Ali M. Al-Radaideh. PhDDepartment of Medical ImagingFaculty of Allied
Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5
390 ext.5422, 5355, 5364Email: ali.radai...@hu.edu.jo
*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
*
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[Freesurfer] GLM fitting for the cortical volume

[Ali Radaideh]

Dear FS experts,

I have managed to run the *glm_fit* on the cortical thickness and area on a
group of MS patients. However, i am not sure how to do this on the cortical
volume. which file represents the cortical volume in subject's directory?

Many thanks,

-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo *
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
*
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Re: [Freesurfer] Cortical thickness_Group analysis

[Ali Radaideh]

Dear Douglas,

Can I check with you if you have received my reply below to your question??

Thanks,
Ali


On Mon, Jun 5, 2017 at 10:16 PM Ali Radaideh <ali.radai...@hu.edu.jo> wrote:

> Thanks alot.
>
> Below are the commands I used in order:
>
> mris_preproc --fsgd disease_Healthy_Age.fsgd --target fsaverage --hemi lh
> --meas thickness --out lh.disease_Healthy_Age.thickness.00.mgh
>
> mri_surf2surf --hemi lh --s fsaverage --sval
> lh.disease_Healthy_Age.thickness.00.mgh --fwhm 10 --cortex --tval
> lh.disease_Healthy_Age.thickness.10.mgh
>
>
> mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd
> disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C
> lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C
> lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf
> fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir
>
>
> mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg --cwp
>  0.05 --2spaces
>
> On Mon, Jun 5, 2017 at 4:03 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
> wrote:
>
>> what is your mri_glmfit command?
>>
>> On 6/4/17 8:10 PM, Ali Radaideh wrote:
>>
>> Dear FS experts,
>>
>> I am trying to analyse the cortical thickness for a group of MS patients
>> and healthy controls. I have followed the instructions on how to perform
>> group analysis but I am still unable to achieve what I am looking for.
>>
>> I am trying to produce a significance map to show the cortical areas that
>> are statistically different between MS and healthy controls (in terms of
>> cortical thickness).
>>
>> Would it be possible please to show you the matrix (fsgd) and contrasts
>> files that I have used in my analysis?
>>
>> Best regards and many thanks in advance,
>>
>> Ali
>>
>> --
>>
>>
>>
>>
>>
>>
>>
>> *Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean
>> of the Faculty of Allied Health Sciences The Hashemite University,  Zarqa,
>> Jordan W.phone +962 5 390 ext.5422, 5355, 5364 Email:
>> ali.radai...@hu.edu.jo <ali.radai...@hu.edu.jo> *
>> *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
>> <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*
>>
>>
>>
>> ___
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>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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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.
>>
>>
>
>
> --
>
>
>
>
>
>
>
> *Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
> the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
> JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
> ali.radai...@hu.edu.jo <ali.radai...@hu.edu.jo>*
> *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
> <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*
>
> --
Sent from iPhone
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Re: [Freesurfer] Cortical thickness_Group analysis

[Ali Radaideh]

Thanks alot.

Below are the commands I used in order:

mris_preproc --fsgd disease_Healthy_Age.fsgd --target fsaverage --hemi lh
--meas thickness --out lh.disease_Healthy_Age.thickness.00.mgh

mri_surf2surf --hemi lh --s fsaverage --sval
lh.disease_Healthy_Age.thickness.00.mgh --fwhm 10 --cortex --tval
lh.disease_Healthy_Age.thickness.10.mgh


mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd
disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C
lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C
lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf
fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir


mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg --cwp
 0.05 --2spaces

On Mon, Jun 5, 2017 at 4:03 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> what is your mri_glmfit command?
>
> On 6/4/17 8:10 PM, Ali Radaideh wrote:
>
> Dear FS experts,
>
> I am trying to analyse the cortical thickness for a group of MS patients
> and healthy controls. I have followed the instructions on how to perform
> group analysis but I am still unable to achieve what I am looking for.
>
> I am trying to produce a significance map to show the cortical areas that
> are statistically different between MS and healthy controls (in terms of
> cortical thickness).
>
> Would it be possible please to show you the matrix (fsgd) and contrasts
> files that I have used in my analysis?
>
> Best regards and many thanks in advance,
>
> Ali
>
> --
>
>
>
>
>
>
>
> *Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean
> of the Faculty of Allied Health Sciences The Hashemite University,  Zarqa,
> Jordan W.phone +962 5 390 ext.5422, 5355, 5364 Email:
> ali.radai...@hu.edu.jo <ali.radai...@hu.edu.jo> *
> *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
> <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*
>
>
>
> ___
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>
>
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> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo <ali.radai...@hu.edu.jo>*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
<http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*
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[Freesurfer] Cortical thickness_Group analysis

[Ali Radaideh]

Dear FS experts,

I am trying to analyse the cortical thickness for a group of MS patients
and healthy controls. I have followed the instructions on how to perform
group analysis but I am still unable to achieve what I am looking for.

I am trying to produce a significance map to show the cortical areas that
are statistically different between MS and healthy controls (in terms of
cortical thickness).

Would it be possible please to show you the matrix (fsgd) and contrasts
files that I have used in my analysis?

Best regards and many thanks in advance,

Ali

-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo *
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
*


disease_Healthy_Age.fsgd
Description: Binary data


lh-MS_vs_Healthy.mtx
Description: Binary data


lh-female_MS_vs_Healthy.mtx
Description: Binary data


lh-female_MS_vs_Healthy_Age.mtx
Description: Binary data


lh-male_MS_vs_Healthy.mtx
Description: Binary data


lh-male_MS_vs_Healthy_Age.mtx
Description: Binary data
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[Freesurfer] cortex mask

[Ali Radaideh]

Dear FreeSurfer Experts,

We have two high resolution datasets (T1 and T2* images). T2* is
co-registered to the T1 volume. The T1 volume was processed in freesurfer
using the recon-all and we want to use the segmented cortex (by freesurfer)
as a mask to extract the cortex from the T2* volume.

Would it be possible, please, to let us know which command to use to
transfer the segmented cortex to the native space of T1 and T2*?.

Many thanks in advance,
Ali

-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo *
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
*
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Re: [Freesurfer] Parcellation stats

[Ali Radaideh]

I am trying to extract the cortical volume, thickness, and area based on
these 17Networks cortical parcellation.

Thanks,
Ali

On Fri, Oct 2, 2015 at 6:23 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> You should not use both --seg and --annot. What are you trying to
> accomplish?
>
> On 10/2/15 3:34 AM, Ali Radaideh wrote:
>
> Hi Bruce,
>
> I have used the following command line:
>
> mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh
> lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum
>
> and got the following:
>
> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName
>   1   0  15766121 15766121.0  Seg
>   2   2182848   182848.0  Seg0002
>   3   3215011   215011.0  Seg0003
>   4   4  6547 6547.0  Seg0004
>   5   5   572  572.0  Seg0005
>   6   7 1405314053.0  Seg0007
>   7   8 4777947779.0  Seg0008
>   8  10  7151 7151.0  Seg0010
>   9  11  4464 4464.0  Seg0011
>  10  12  5264 5264.0  Seg0012
>  11  13  1680 1680.0  Seg0013
>  12  14   889  889.0  Seg0014
>  13  15  1731 1731.0  Seg0015
>  14  16 1730717307.0  Seg0016
>  15  17  3842 3842.0  Seg0017
>  16  18  1106 1106.0  Seg0018
>  17  24  1228 1228.0  Seg0024
>  18  26   656  656.0  Seg0026
>  19  28  3941 3941.0  Seg0028
>  20  3026   26.0  Seg0030
>  21  31  1222 1222.0  Seg0031
>  22  41191593   191593.0  Seg0041
>  23  42200955   200955.0  Seg0042
>  24  43  6321 6321.0  Seg0043
>  25  44   295  295.0  Seg0044
>  26  46 1610616106.0  Seg0046
>  27  47 4647246472.0  Seg0047
>  28  49  6684 6684.0  Seg0049
>  29  50  4308 4308.0  Seg0050
>  30  51  5099 5099.0  Seg0051
>  31  52  1459 1459.0  Seg0052
>  32  53  4005 4005.0  Seg0053
>  33  54   988  988.0  Seg0054
>  34  58   633  633.0  Seg0058
>  35  60  3554 3554.0  Seg0060
>  36  6236   36.0  Seg0062
>  37  63  1518 1518.0  Seg0063
>  38  7218   18.0  Seg0072
>  39  77  1040 1040.0  Seg0077
>  40  8022   22.0  Seg0080
>  41  85   124  124.0  Seg0085
>  42 251   721  721.0  Seg0251
>  43 252   403  403.0  Seg0252
>  44 253   322  322.0  Seg0253
>  45 254   360  360.0  Seg0254
>  46 255   742  742.0  Seg0255
>
>
> However,
> I don't see the segmentation names (cortical parts). is my command true/
> complete or not?
> These are 46 segmentations although I am using 17 networks cortical
> parcellation, is this true?
> Can I add anything to make the output more informative?. Also can I get
> any surface area etc?
>
>
>
> Many thanks in advance.
> Ali
>
> On Thu, Oct 1, 2015 at 10:43 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>
>> sure, you can use mri_segstats to get stats from it
>> Bruce
>> On Thu, 1 Oct 2015, Ali Radaideh wrote:
>>
>> Can we get any stats from this type of parcellation? I only can see two
>>> annotation files after running the mri_surf2surf command and these can be
>>> loaded tksurfer as an overlay.
>>>
>>>
>>> Thanks,
>>> Ali
>>>
>>> On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   that will generate a parcellation on the individual subject
>>>   surface of Thomas Yeo's 17-network clustering. It won't do
>>>   anything with the thickness though. What are you trying to do?
>>>
>>>   On Tue, 29 Sep 2015, Ali Radaideh wrote:
>>>
>>> mri_surf2surf --srcsubject fsaverage --trgsubject
>>> scz10 --hemi rh
>>>
>>> --sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks
>>> _N1000.annot
>>> --tval
>>> $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
>>>
>>> scz10 is my subject name
>>>
>>> On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve
>>> <gr...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   what is your surf2surf command?
>>>
>>>   On 9/28/15 5:11 PM, Ali Radaideh wrote:
>>>   Dear Douglas,
>>>
>>> Thanks for your email. I meant to say that after
>>> running the
>>> recon-all, i ran the sur2sur

Re: [Freesurfer] Group Analysis

[Ali Radaideh]

Sorry, as I am quite new to this type of analysis, does the sig.mgh show
any significance? if so how can I report it? I mean are they saved
somewhere in SUBJECTS_DIR?

Also, it seems the corrected one does not show anything, am I true?

The last thing about this, shall I use sig.mgh or F.mgh?

Many thanks for your great help.
Ali

On Fri, Oct 2, 2015 at 8:25 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> what about them?
>
> On 10/2/15 1:20 PM, Ali Radaideh wrote:
>
> Thanks Douglas,
>
> The second line worked fine, but can I show you the results attached to
> this email?
>
>
>
> Thanks,
> Ali
>
> On Fri, Oct 2, 2015 at 7:22 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
> wrote:
>
>> I notice from the image that the overlay is turned off. Try turning it
>> on. Also, you can try
>>
>> tksurferfv fsaverage lh inflated -aparc -ov sig.mgh
>>
>> If that does not work, then
>>
>> tksurfer fsaverage lh inflated -aparc -ov sig.mgh
>>
>>
>> On 10/2/15 12:08 PM, Ali Radaideh wrote:
>>
>> Hi,
>>
>> I am running a group analysis (patients versus controls). I am following
>> the tutorial and managed to create the FSGD file with four classes
>> MSMale
>> MSFemale
>> HealthyMale
>> HealthyFemale
>>
>> and one variable: Age
>>
>>
>> So the number of NregressorsDODS is equal to 8
>>
>> [ MSMale MSFemale HealthyMale HealthyFemale  Age_ MSMale  Age_ MSFemale
>>  Age_ HealthyMale  Age_ HealthyFemale ]
>>
>> I have created my own contrast files as follows:
>>
>> lh-female_MS_vs_Healthy
>> ​ .mtx
>> * to  *
>> * compare between Female MS and Female Healthy regardless of age *:
>> *[ 0 1 0 -1 0 0 0 0 ]​*
>>
>>
>> *lh-female_MS_vs_Healthy_Age ​ .mtx *
>> * ​​   *
>> ​
>> * to  *
>> * compare between Female MS and Female Healthy_with age effect *:
>> * ​[​ 0 0 0 0 0 1 0 -1 ​] *
>>
>> *lh-male_MS_vs_Healthy ​ .mtx*
>> ​
>> * to  *
>> * compare between Male MS and Male Healthy regardless of age *:
>>
>> * ​[ ​ 1 0 -1 0 0 0 0 0 ​] ​ *
>>
>> *lh-male_MS_vs_Healthy_Age ​ .mtx​  to  *
>> * compare between Male MS and Male Healthy_with age effect *
>>   :
>> * [ 0 0 0 0 1 0 -1 0  ​ ]​ *
>>
>> * ​ *
>> * ​ *
>> *lh-MS_vs_Healthy ​ .mtx​   to compare between MS and Healthy regardless
>> of Age and Gender *:
>> * ​ [  0.5 0.5 -0.5 -0.5 0 0 0 0  ] ​ *
>>
>>
>> * I ran the glm_fit using the following command line: *
>>
>> * mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd
>> disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C
>> lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C
>> lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf
>> fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir *
>>
>>
>> * Everything went OK except when loading the sig.mgh in freeview using
>> the following command: *
>>
>>
>> * freeview -f
>> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh:overlay_threshold=4,5
>> -viewport 3d 1- It complained that the flag  annot_outline=1 is not
>> recognized 2- after removing this flag from the command line, t he overlay
>> only was two colors (green and red) (I have attached a copy of it)  *
>>
>> * ​ Then I did * a cluster-wise correction for multiple comparisons
>> ​ by​
>> run
>> ​ n​
>> ing​
>> a simulation
>> * ​ as follows: *
>>
>> * mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg
>> --cwp  0.05 --2spaces *
>>
>> * Nothing has changed. in free view the same overlay. *
>>
>> * I opened the   " *cache.th40.neg.sig.cluster.summary
>> ​" file​
>> ​ and got the following:
>>
>> # Cluster Growing Summary (mri_surfcluster)
>> # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
>> # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
>> # CreationTime 2015/10/02-15:06:07-GMT
>> # cmdline mri_surfcluster --in
>> lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh --csd
>> /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/neg/th40/mc-z.csd
>> --mask lh.disease_Healthy_Age.glmdir/mask.mgh --cwsig
>> lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.cluster.mgh
>> --vwsig
>> lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.voxel.mgh
>

Re: [Freesurfer] Parcellation stats

[Ali Radaideh]

Hi Bruce,

I have used the following command line:

mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh
lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum

and got the following:

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName
  1   0  15766121 15766121.0  Seg
  2   2182848   182848.0  Seg0002
  3   3215011   215011.0  Seg0003
  4   4  6547 6547.0  Seg0004
  5   5   572  572.0  Seg0005
  6   7 1405314053.0  Seg0007
  7   8 4777947779.0  Seg0008
  8  10  7151 7151.0  Seg0010
  9  11  4464 4464.0  Seg0011
 10  12  5264 5264.0  Seg0012
 11  13  1680 1680.0  Seg0013
 12  14   889  889.0  Seg0014
 13  15  1731 1731.0  Seg0015
 14  16 1730717307.0  Seg0016
 15  17  3842 3842.0  Seg0017
 16  18  1106 1106.0  Seg0018
 17  24  1228 1228.0  Seg0024
 18  26   656  656.0  Seg0026
 19  28  3941 3941.0  Seg0028
 20  3026   26.0  Seg0030
 21  31  1222 1222.0  Seg0031
 22  41191593   191593.0  Seg0041
 23  42200955   200955.0  Seg0042
 24  43  6321 6321.0  Seg0043
 25  44   295  295.0  Seg0044
 26  46 1610616106.0  Seg0046
 27  47 4647246472.0  Seg0047
 28  49  6684 6684.0  Seg0049
 29  50  4308 4308.0  Seg0050
 30  51  5099 5099.0  Seg0051
 31  52  1459 1459.0  Seg0052
 32  53  4005 4005.0  Seg0053
 33  54   988  988.0  Seg0054
 34  58   633  633.0  Seg0058
 35  60  3554 3554.0  Seg0060
 36  6236   36.0  Seg0062
 37  63  1518 1518.0  Seg0063
 38  7218   18.0  Seg0072
 39  77  1040 1040.0  Seg0077
 40  8022   22.0  Seg0080
 41  85   124  124.0  Seg0085
 42 251   721  721.0  Seg0251
 43 252   403  403.0  Seg0252
 44 253   322  322.0  Seg0253
 45 254   360  360.0  Seg0254
 46 255   742  742.0  Seg0255


However,
I don't see the segmentation names (cortical parts). is my command true/
complete or not?
These are 46 segmentations although I am using 17 networks cortical
parcellation, is this true?
Can I add anything to make the output more informative?. Also can I get any
surface area etc?



Many thanks in advance.
Ali

On Thu, Oct 1, 2015 at 10:43 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> sure, you can use mri_segstats to get stats from it
> Bruce
> On Thu, 1 Oct 2015, Ali Radaideh wrote:
>
> Can we get any stats from this type of parcellation? I only can see two
>> annotation files after running the mri_surf2surf command and these can be
>> loaded tksurfer as an overlay.
>>
>>
>> Thanks,
>> Ali
>>
>> On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu
>> >
>> wrote:
>>   that will generate a parcellation on the individual subject
>>   surface of Thomas Yeo's 17-network clustering. It won't do
>>   anything with the thickness though. What are you trying to do?
>>
>>   On Tue, 29 Sep 2015, Ali Radaideh wrote:
>>
>> mri_surf2surf --srcsubject fsaverage --trgsubject
>> scz10 --hemi rh
>>
>> --sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks
>> _N1000.annot
>> --tval
>> $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
>>
>> scz10 is my subject name
>>
>> On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve
>> <gr...@nmr.mgh.harvard.edu>
>> wrote:
>>   what is your surf2surf command?
>>
>>   On 9/28/15 5:11 PM, Ali Radaideh wrote:
>>   Dear Douglas,
>>
>> Thanks for your email. I meant to say that after
>> running the
>> recon-all, i ran the sur2surf command to get the
>> cortical
>> parcellation using Thomas Yeo Atlas.
>>
>> I thought that the extracted cortical thickness
>> after running
>> the surf2surf command will be different from the one
>> extracted
>> before running the command. But, Bruce kindly
>> replied to my
>> email saying that it is the same if it is calculated
>> on
>> vertex-wise basis.
>>
>> Thanks,
>> Ali
>>
>> On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve
>> <gr...@nmr.mgh.harvard.edu> wrote:
>>   I can't understand what you are asking. Can
>> you
>>   el

Re: [Freesurfer] Parcellation stats

[Ali Radaideh]

Can we get any stats from this type of parcellation? I only can see two
annotation files after running the mri_surf2surf command and these can be
loaded tksurfer as an overlay.


Thanks,
Ali

On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> that will generate a parcellation on the individual subject surface of
> Thomas Yeo's 17-network clustering. It won't do anything with the thickness
> though. What are you trying to do?
>
> On Tue, 29 Sep 2015, Ali Radaideh wrote:
>
> mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh
>>
>> --sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot
>> --tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
>>
>> scz10 is my subject name
>>
>> On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu
>> >
>> wrote:
>>   what is your surf2surf command?
>>
>>   On 9/28/15 5:11 PM, Ali Radaideh wrote:
>>   Dear Douglas,
>>
>> Thanks for your email. I meant to say that after running the
>> recon-all, i ran the sur2surf command to get the cortical
>> parcellation using Thomas Yeo Atlas.
>>
>> I thought that the extracted cortical thickness after running
>> the surf2surf command will be different from the one extracted
>> before running the command. But, Bruce kindly replied to my
>> email saying that it is the same if it is calculated on
>> vertex-wise basis.
>>
>> Thanks,
>> Ali
>>
>> On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve
>> <gr...@nmr.mgh.harvard.edu> wrote:
>>   I can't understand what you are asking. Can you
>>   elaborate?
>>
>>   On 09/28/2015 01:51 PM, Ali Radaideh wrote:
>>   > Thanks alot Douglas,
>>   >
>>   > Yes it is there but after checking it many time I
>>   found it corrupted
>>   > for some subjects due to copying them many times
>>   between machines.
>>   >
>>   > But May I ask you some thing related. I have just
>>   posted a question
>>   > regarding getting the cortical thickness after
>>   running the surf2surf
>>   > command (17 networks cortical parcellation). Now I
>>   found the stats
>>   > file not updated after running this command only
>>   the annotation files
>>   > in label folder.
>>   [rh.Yeo2011_17Networks_N1000.annot]. We thought that
>>   > using Yeo Atlas will give slightly different
>>   cortical thickness, are
>>   > we correct?
>>   >
>>   > Thanks,
>>   > Ali
>>   >
>>   > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve
>>   > <gr...@nmr.mgh.harvard.edu
>>   <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>   >
>>   > does that file exist?
>>   >
>>   > On 09/28/2015 01:05 PM, Ali Radaideh wrote:
>>   > > Dear FreeSurfer experts,
>>   > > After finishing the recon-all, I am trying
>>   to extract the cortical
>>   > > thickness for each subject and group them
>>   into one table but
>>   > > unfortunately i keep getting the following
>>   error:
>>   > >
>>   > > ​rh.aparc.DKTatlas40.stats is not found or is
>>   too small to be a
>>   > valid
>>   > > statsfile
>>   > > Use --skip flag to automatically skip bad
>>   stats files​
>>   > >
>>   > > i tried to change the stats file (e.g I used
>>   aparc.a2009s) but I got
>>   > > the same error.
>>   > >
>>   > > I tried each brain alone and also got the
>>   same error.
>>   > >
>>   > > Any ideas please
>>   > > ​Thanks,
>>   > > Ali​
>>   > >
>>   > > --
>>   > > /Ali M. Al-Radaideh. PhD
>>   > > Head of Department of Medical Imaging
>>   > > Vice Dean of the Faculty of Allied Health
>>   Sciences
>>   > > The Hashemite University,
>>   > > Zarqa, Jordan
>>   > > W.phone +962 5 390 ext.5422, 5355, 5364
>>   > > Email: ali.radai...@hu.edu.jo
>>   <mailto:ali.radai...@hu.edu.jo>
>>   

Re: [Freesurfer] Parcellation stats

[Ali Radaideh]

mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh
--sval-annot
$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot
--tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot

scz10 is my subject name

On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> what is your surf2surf command?
>
> On 9/28/15 5:11 PM, Ali Radaideh wrote:
>
> Dear Douglas,
>
> Thanks for your email. I meant to say that after running the recon-all, i
> ran the sur2surf command to get the cortical parcellation using Thomas Yeo
> Atlas.
>
> I thought that the extracted cortical thickness after running the
> surf2surf command will be different from the one extracted before running
> the command. But, Bruce kindly replied to my email saying that it is the
> same if it is calculated on vertex-wise basis.
>
> Thanks,
> Ali
>
> On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> I can't understand what you are asking. Can you elaborate?
>>
>> On 09/28/2015 01:51 PM, Ali Radaideh wrote:
>> > Thanks alot Douglas,
>> >
>> > Yes it is there but after checking it many time I found it corrupted
>> > for some subjects due to copying them many times between machines.
>> >
>> > But May I ask you some thing related. I have just posted a question
>> > regarding getting the cortical thickness after running the surf2surf
>> > command (17 networks cortical parcellation). Now I found the stats
>> > file not updated after running this command only the annotation files
>> > in label folder. [rh.Yeo2011_17Networks_N1000.annot]. We thought that
>> > using Yeo Atlas will give slightly different cortical thickness, are
>> > we correct?
>> >
>> > Thanks,
>> > Ali
>> >
>> > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve
>> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> >
>> > does that file exist?
>> >
>> > On 09/28/2015 01:05 PM, Ali Radaideh wrote:
>> > > Dear FreeSurfer experts,
>> > > After finishing the recon-all, I am trying to extract the cortical
>> > > thickness for each subject and group them into one table but
>> > > unfortunately i keep getting the following error:
>> > >
>> > > ​ rh.aparc.DKTatlas40.stats is not found or is too small to be a
>> > valid
>> > > statsfile
>> > > Use --skip flag to automatically skip bad stats files​
>> > >
>> > > i tried to change the stats file (e.g I used aparc.a2009s) but I
>> got
>> > > the same error.
>> > >
>> > > I tried each brain alone and also got the same error.
>> > >
>> > > Any ideas please
>> > > ​Thanks,
>> > > Ali​
>> > >
>> > > --
>> > > /Ali M. Al-Radaideh. PhD
>> > > Head of Department of Medical Imaging
>> > > Vice Dean of the Faculty of Allied Health Sciences
>> > > The Hashemite University,
>> > > Zarqa, Jordan
>> > > W.phone +962 5 390 ext.5422, 5355, 5364
>> > > Email: ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo>
>> > <mailto:ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo>>
>> > > /
>> > > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
>> > >
>> > >
>> > >
>> > > ___
>> > > Freesurfer mailing list
>> > > Freesurfer@nmr.mgh.harvard.edu
>> > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu>
>> > Phone Number: 617-724-2358
>> > Fax: 617-726-7422
>> >
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> > Outgoing:
>> >   

Re: [Freesurfer] Cortical Parcellation_Yeo_networks

[Ali Radaideh]

Hi Thomas,

I have done the mri_surf2surf all all old data and everything went OK.
Thanks for your help.

Now I need to extract the NEW cortical thickness based on this new
parcellation. I am saying NEW because I extracted the cortical thickness
last year without running the mri_surf2surf. We think the new cortical
thickness will be different from the one we extracted last year due to the
use of new ATLAS. Are we correct?

Many thanks in advance,
Ali

On Sun, Sep 20, 2015 at 3:33 AM, Thomas Yeo <
> ​​
> ytho...@csail.mit.edu> wrote:
>
>> Hi Ali,
>>
>> It should work with the old processed data.
>>
>> --Thomas
>>
>> On Sun, Sep 20, 2015 at 12:00 AM, Ali Radaideh <ali.radai...@hu.edu.jo>
>> wrote:
>> > Dear Thomas,
>> >
>> > Many thanks for your detailed explanation. I will try it and let you
>> know.
>> >
>> > One more question please, last year, I processed another set of subjects
>> > using an older version of FreeSurfer 5.0. Now the old version has been
>> > replaced with its new one (5.3.0) on the same PC. In other words, my PC
>> has
>> > the new version of freesurfer 5.3.0 and two sets of processed T1
>> images. One
>> > set was processed using the old version of freesurfer which is no longer
>> > there. The other set was processed using the new version. So, can I
>> > transform the network atlases to the set of subjects spaces processed
>> last
>> > year using the old version of freesurfe 5.0.0r? or or I have to re-run
>> the
>> > recon-all again?
>> >
>> > Many thanks in advance and my apology for keeping you busy with my
>> > questions.
>> >
>> > Ali
>> >
>> >
>> > On Sat, Sep 19, 2015 at 3:14 PM, Thomas Yeo <ytho...@csail.mit.edu>
>> wrote:
>> >>
>> >> Hi Ali,
>> >>
>> >> Sorry, I wasn't clear. The 7 and 17 network atlases are released with
>> >> FreeSurfer 5.3. In particular, the "annot" files are found in
>> >> $FREESURFER_HOME/subjects/fsaverage/label/. Therefore since you have
>> >> already run recon-all using FreeSurfer, then this means that you do
>> >> not need to "save" the new atlas anywhere.
>> >>
>> >> The 7 and 17 network atlases are in fsaverage space. You can run the
>> >> following commands to transform the atlases to your individual
>> >> subjects' surfaces. Suppose your subject is called 100306_QD95CU_FS
>> >> and the recon-all of this subject is located in
>> >> /share/users/imganalysis/yeolab/data/GSP/.
>> >>
>> >> 1) The first step is to set the variable SUBJECTS_DIR to point to
>> >> where your subject is:
>> >>
>> >> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
>> >>
>> >> 2) The second step is to create a symbolic link so that the FreeSurfer
>> >> "fsaverage" subject appears to be in your SUBJECTS_DIR
>> >>
>> >> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
>> >>
>> >> 3) The final step is to run mri_surf2surf to transform the 7 network
>> >> atlas to your subject's native surfaces.
>> >>
>> >> >> mri_surf2surf --srcsubject fsaverage --trgsubject 100306_QD95CU_FS
>> >> >> --hemi lh --sval-annot
>> >> >>
>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
>> >> >> --tval
>> $SUBJECTS_DIR/100306_QD95CU_FS/label/lh.Yeo2011_7Networks_N1000.annot
>> >>
>> >> Note that the above is only for the left hemisphere. You can replace
>> >> all the "lh" with "rh" to transform the right hemisphere instead.
>> >>
>> >> Note that the above is for the 7 networks. You can replace all the "7"
>> >> with "17" to transform the 17-network atlas instead.
>> >>
>> >> I hope the above is clearer. Let me know if you have other questions.
>> >>
>> >> --Thomas
>> >>
>> >> On Sat, Sep 19, 2015 at 4:16 PM, Ali Radaideh <ali.radai...@hu.edu.jo>
>> >> wrote:
>> >> > Also, could you please direct me in which directory I should save the
>> >> > new
>> >> > atlas?
>> >> >
>> >> > Thanks,
>> >> > Ali
>> >> >
>> >> > On Sat, Sep 19, 2015 at 9:47 AM, Thomas Ye

Re: [Freesurfer] Parcellation stats

[Ali Radaideh]

Thanks alot Douglas,

Yes it is there but after checking it many time I found it corrupted for
some subjects due to copying them many times between machines.

But May I ask you some thing related. I have just posted a question
regarding getting the cortical thickness after running the surf2surf
command (17 networks cortical parcellation). Now I found the stats file not
updated after running this command only the annotation files in label
folder. [rh.Yeo2011_17Networks_N1000.annot]. We thought that using Yeo
Atlas will give slightly different cortical thickness, are we correct?

Thanks,
Ali

On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> does that file exist?
>
> On 09/28/2015 01:05 PM, Ali Radaideh wrote:
> > Dear FreeSurfer experts,
> > After finishing the recon-all, I am trying to extract the cortical
> > thickness for each subject and group them into one table but
> > unfortunately i keep getting the following error:
> >
> > ​ rh.aparc.DKTatlas40.stats is not found or is too small to be a valid
> > statsfile
> > Use --skip flag to automatically skip bad stats files​
> >
> > i tried to change the stats file (e.g I used aparc.a2009s) but I got
> > the same error.
> >
> > I tried each brain alone and also got the same error.
> >
> > Any ideas please
> > ​Thanks,
> > Ali​
> >
> > --
> > /Ali M. Al-Radaideh. PhD
> > Head of Department of Medical Imaging
> > Vice Dean of the Faculty of Allied Health Sciences
> > The Hashemite University,
> > Zarqa, Jordan
> > W.phone +962 5 390 ext.5422, 5355, 5364
> > Email: ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo>
> > /
> > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
> >
> >
> >
> > ___
> > 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
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-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo <ali.radai...@hu.edu.jo>*
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Re: [Freesurfer] Cortical Parcellation_Yeo_networks

[Ali Radaideh]

Hi Thomas,

I have done the mri_surf2surf all all old data and everything went OK.
Thanks for your help.

Now I need to extract the NEW cortical thickness based on this new
parcellation. I am saying NEW because I extracted the cortical thickness
last year without running the mri_surf2surf. We think the new cortical
thickness will be different from the one we extracted last year due to the
use of new ATLAS. Are we correct?

Many thanks in advance,
Ali

On Sun, Sep 20, 2015 at 3:33 AM, Thomas Yeo <ytho...@csail.mit.edu> wrote:

> Hi Ali,
>
> It should work with the old processed data.
>
> --Thomas
>
> On Sun, Sep 20, 2015 at 12:00 AM, Ali Radaideh <ali.radai...@hu.edu.jo>
> wrote:
> > Dear Thomas,
> >
> > Many thanks for your detailed explanation. I will try it and let you
> know.
> >
> > One more question please, last year, I processed another set of subjects
> > using an older version of FreeSurfer 5.0. Now the old version has been
> > replaced with its new one (5.3.0) on the same PC. In other words, my PC
> has
> > the new version of freesurfer 5.3.0 and two sets of processed T1 images.
> One
> > set was processed using the old version of freesurfer which is no longer
> > there. The other set was processed using the new version. So, can I
> > transform the network atlases to the set of subjects spaces processed
> last
> > year using the old version of freesurfe 5.0.0r? or or I have to re-run
> the
> > recon-all again?
> >
> > Many thanks in advance and my apology for keeping you busy with my
> > questions.
> >
> > Ali
> >
> >
> > On Sat, Sep 19, 2015 at 3:14 PM, Thomas Yeo <ytho...@csail.mit.edu>
> wrote:
> >>
> >> Hi Ali,
> >>
> >> Sorry, I wasn't clear. The 7 and 17 network atlases are released with
> >> FreeSurfer 5.3. In particular, the "annot" files are found in
> >> $FREESURFER_HOME/subjects/fsaverage/label/. Therefore since you have
> >> already run recon-all using FreeSurfer, then this means that you do
> >> not need to "save" the new atlas anywhere.
> >>
> >> The 7 and 17 network atlases are in fsaverage space. You can run the
> >> following commands to transform the atlases to your individual
> >> subjects' surfaces. Suppose your subject is called 100306_QD95CU_FS
> >> and the recon-all of this subject is located in
> >> /share/users/imganalysis/yeolab/data/GSP/.
> >>
> >> 1) The first step is to set the variable SUBJECTS_DIR to point to
> >> where your subject is:
> >>
> >> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
> >>
> >> 2) The second step is to create a symbolic link so that the FreeSurfer
> >> "fsaverage" subject appears to be in your SUBJECTS_DIR
> >>
> >> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
> >>
> >> 3) The final step is to run mri_surf2surf to transform the 7 network
> >> atlas to your subject's native surfaces.
> >>
> >> >> mri_surf2surf --srcsubject fsaverage --trgsubject 100306_QD95CU_FS
> >> >> --hemi lh --sval-annot
> >> >>
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
> >> >> --tval
> $SUBJECTS_DIR/100306_QD95CU_FS/label/lh.Yeo2011_7Networks_N1000.annot
> >>
> >> Note that the above is only for the left hemisphere. You can replace
> >> all the "lh" with "rh" to transform the right hemisphere instead.
> >>
> >> Note that the above is for the 7 networks. You can replace all the "7"
> >> with "17" to transform the 17-network atlas instead.
> >>
> >> I hope the above is clearer. Let me know if you have other questions.
> >>
> >> --Thomas
> >>
> >> On Sat, Sep 19, 2015 at 4:16 PM, Ali Radaideh <ali.radai...@hu.edu.jo>
> >> wrote:
> >> > Also, could you please direct me in which directory I should save the
> >> > new
> >> > atlas?
> >> >
> >> > Thanks,
> >> > Ali
> >> >
> >> > On Sat, Sep 19, 2015 at 9:47 AM, Thomas Yeo <ytho...@csail.mit.edu>
> >> > wrote:
> >> >>
> >> >> Hi Ali,
> >> >>
> >> >> May I confirm that your data is T1 and not functional data? Here's
> >> >> what you can do to transfer the parcellation to your individual
> >> >> subject's surface mesh. After that you can use the usual

[Freesurfer] Parcellation stats

[Ali Radaideh]

Dear FreeSurfer experts,
After finishing the recon-all, I am trying to extract the cortical
thickness for each subject and group them into one table but unfortunately
i keep getting the following error:

​rh.aparc.DKTatlas40.stats is not found or is too small to be a valid
statsfile
Use --skip flag to automatically skip bad stats files​

i tried to change the stats file (e.g I used aparc.a2009s) but I got the
same error.

I tried each brain alone and also got the same error.

Any ideas please
​Thanks,
Ali​

-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo *
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
*
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Re: [Freesurfer] Parcellation stats

[Ali Radaideh]

Dear Douglas,

Thanks for your email. I meant to say that after running the recon-all, i
ran the sur2surf command to get the cortical parcellation using Thomas Yeo
Atlas.

I thought that the extracted cortical thickness after running the surf2surf
command will be different from the one extracted before running the
command. But, Bruce kindly replied to my email saying that it is the same
if it is calculated on vertex-wise basis.

Thanks,
Ali

On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> wrote:

> I can't understand what you are asking. Can you elaborate?
>
> On 09/28/2015 01:51 PM, Ali Radaideh wrote:
> > Thanks alot Douglas,
> >
> > Yes it is there but after checking it many time I found it corrupted
> > for some subjects due to copying them many times between machines.
> >
> > But May I ask you some thing related. I have just posted a question
> > regarding getting the cortical thickness after running the surf2surf
> > command (17 networks cortical parcellation). Now I found the stats
> > file not updated after running this command only the annotation files
> > in label folder. [rh.Yeo2011_17Networks_N1000.annot]. We thought that
> > using Yeo Atlas will give slightly different cortical thickness, are
> > we correct?
> >
> > Thanks,
> > Ali
> >
> > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > does that file exist?
> >
> > On 09/28/2015 01:05 PM, Ali Radaideh wrote:
> > > Dear FreeSurfer experts,
> > > After finishing the recon-all, I am trying to extract the cortical
> > > thickness for each subject and group them into one table but
> > > unfortunately i keep getting the following error:
> > >
> > > ​ rh.aparc.DKTatlas40.stats is not found or is too small to be a
> > valid
> > > statsfile
> > > Use --skip flag to automatically skip bad stats files​
> > >
> > > i tried to change the stats file (e.g I used aparc.a2009s) but I
> got
> > > the same error.
> > >
> > > I tried each brain alone and also got the same error.
> > >
> > > Any ideas please
> > > ​Thanks,
> > > Ali​
> > >
> > > --
> > > /Ali M. Al-Radaideh. PhD
> > > Head of Department of Medical Imaging
> > > Vice Dean of the Faculty of Allied Health Sciences
> > > The Hashemite University,
> > > Zarqa, Jordan
> > > W.phone +962 5 390 ext.5422, 5355, 5364
> > > Email: ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo>
> > <mailto:ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo>>
> > > /
> > > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://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  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 pat

Re: [Freesurfer] Cortical Parcellation_Yeo_networks

[Ali Radaideh]

Dear Thomas,

Thanks for your email. Our data are whole head T1 weighted images. I am
using tcsh shell.

May I ask you please to simplify your instruction as I am not very familiar
with these things?. However, I can follow any simple instructions and make
the required changes.

Many thanks for your quick reply and help.

Ali

On Sat, Sep 19, 2015 at 9:47 AM, Thomas Yeo <ytho...@csail.mit.edu> wrote:

> Hi Ali,
>
> May I confirm that your data is T1 and not functional data? Here's
> what you can do to transfer the parcellation to your individual
> subject's surface mesh. After that you can use the usual commands to
> extract thickness, etc.
>
> In your shell (assuming you are using c shell)
>
> # First set variable s to be subject id
> >> set s = 100306_QD95CU_FS
>
> # set freesurfer environmental variable SUBJECTS_DIR to point to where
> the data is
> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
>
> # use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR
> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
>
> # use "-sval-annot" option to transfer annotation
> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
> --sval-annot
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
>
> # use "sval" option to transfer confidence map.
> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
>
> Cheers,
> Thomas
>
> On Sat, Sep 19, 2015 at 3:12 PM, Ali Radaideh <ali.radai...@hu.edu.jo>
> wrote:
> > Dear FreeSurfer experts,
> >
> > I have finished processing a group of brains MR images collected at 7T
> > scanner using freesurfer 5.3.0 (Ubuntu 64 bits machine).
> >
> > However, we need to get the cortical parcellation based on functional
> > network connectivity. So I have downloaded the Atlas data
> > (Yeo_JNeurophysiol11_FreeSurfer) to use it for the parcellation but I
> have
> > few questions which I hope you will be able to help me on.
> >
> > 1- Do I need to repeat the "recon-all" process?
> > 2- If yes, how can I change the default Atlas that freesurfer uses?
> > 3- If no, what can I do to get the cortical parcellation based on
> finctional
> > networks from our processed data?
> > 4- At the end, shall I use the usual commands to extract the volumes,
> > thicknesses ...etc?
> >
> >
> > Many thanks for your help in advance.
> >
> > Ali
> >
> >
> > --
> > Ali M. Al-Radaideh. PhD
> > Head of Department of Medical Imaging
> > Vice Dean of the Faculty of Allied Health Sciences
> > The Hashemite University,
> > Zarqa, Jordan
> > W.phone +962 5 390 ext.5422, 5355, 5364
> > Email: ali.radai...@hu.edu.jo
> > webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
> >
> >
> > ___
> > 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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>



-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo <ali.radai...@hu.edu.jo>*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
<http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*
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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
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Re: [Freesurfer] Cortical Parcellation_Yeo_networks

[Ali Radaideh]

Also, could you please direct me in which directory I should save the new
atlas?

Thanks,
Ali

On Sat, Sep 19, 2015 at 9:47 AM, Thomas Yeo <ytho...@csail.mit.edu> wrote:

> Hi Ali,
>
> May I confirm that your data is T1 and not functional data? Here's
> what you can do to transfer the parcellation to your individual
> subject's surface mesh. After that you can use the usual commands to
> extract thickness, etc.
>
> In your shell (assuming you are using c shell)
>
> # First set variable s to be subject id
> >> set s = 100306_QD95CU_FS
>
> # set freesurfer environmental variable SUBJECTS_DIR to point to where
> the data is
> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
>
> # use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR
> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
>
> # use "-sval-annot" option to transfer annotation
> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
> --sval-annot
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
>
> # use "sval" option to transfer confidence map.
> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
>
> Cheers,
> Thomas
>
> On Sat, Sep 19, 2015 at 3:12 PM, Ali Radaideh <ali.radai...@hu.edu.jo>
> wrote:
> > Dear FreeSurfer experts,
> >
> > I have finished processing a group of brains MR images collected at 7T
> > scanner using freesurfer 5.3.0 (Ubuntu 64 bits machine).
> >
> > However, we need to get the cortical parcellation based on functional
> > network connectivity. So I have downloaded the Atlas data
> > (Yeo_JNeurophysiol11_FreeSurfer) to use it for the parcellation but I
> have
> > few questions which I hope you will be able to help me on.
> >
> > 1- Do I need to repeat the "recon-all" process?
> > 2- If yes, how can I change the default Atlas that freesurfer uses?
> > 3- If no, what can I do to get the cortical parcellation based on
> finctional
> > networks from our processed data?
> > 4- At the end, shall I use the usual commands to extract the volumes,
> > thicknesses ...etc?
> >
> >
> > Many thanks for your help in advance.
> >
> > Ali
> >
> >
> > --
> > Ali M. Al-Radaideh. PhD
> > Head of Department of Medical Imaging
> > Vice Dean of the Faculty of Allied Health Sciences
> > The Hashemite University,
> > Zarqa, Jordan
> > W.phone +962 5 390 ext.5422, 5355, 5364
> > Email: ali.radai...@hu.edu.jo
> > webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
> >
> >
> > ___
> > 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
>



-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo <ali.radai...@hu.edu.jo>*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
<http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*
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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.

[Freesurfer] Cortical Parcellation_Yeo_networks

[Ali Radaideh]

Dear FreeSurfer experts,

I have finished processing a group of brains MR images collected at 7T
scanner using freesurfer 5.3.0 (Ubuntu 64 bits machine).

However, we need to get the cortical parcellation based on functional
network connectivity. So I have downloaded the Atlas data
(Yeo_JNeurophysiol11_FreeSurfer) to use it for the parcellation but I have
few questions which I hope you will be able to help me on.

1- Do I need to repeat the "recon-all" process?
2- If yes, how can I change the default Atlas that freesurfer uses?
3- If no, what can I do to get the cortical parcellation based on
finctional networks from our processed data?
4- At the end, shall I use the usual commands to extract the volumes,
thicknesses ...etc?


Many thanks for your help in advance.

Ali


-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo *
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
*
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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] Cortical Parcellation_Yeo_networks

[Ali Radaideh]

Dear Thomas,

Many thanks for your detailed explanation. I will try it and let you know.

One more question please, last year, I processed another set of subjects
using an older version of FreeSurfer 5.0. Now the old version has been
replaced with its new one (5.3.0) on the same PC. In other words, my PC has
the new version of freesurfer 5.3.0 and two sets of processed T1 images.
One set was processed using the old version of freesurfer which is no
longer there. The other set was processed using the new version. So, can I
transform the network atlases to the set of subjects spaces processed last
year using the old version of freesurfe 5.0.0r? or or I have to re-run the
recon-all again?

Many thanks in advance and my apology for keeping you busy with my
questions.

Ali


On Sat, Sep 19, 2015 at 3:14 PM, Thomas Yeo <ytho...@csail.mit.edu> wrote:

> Hi Ali,
>
> Sorry, I wasn't clear. The 7 and 17 network atlases are released with
> FreeSurfer 5.3. In particular, the "annot" files are found in
> $FREESURFER_HOME/subjects/fsaverage/label/. Therefore since you have
> already run recon-all using FreeSurfer, then this means that you do
> not need to "save" the new atlas anywhere.
>
> The 7 and 17 network atlases are in fsaverage space. You can run the
> following commands to transform the atlases to your individual
> subjects' surfaces. Suppose your subject is called 100306_QD95CU_FS
> and the recon-all of this subject is located in
> /share/users/imganalysis/yeolab/data/GSP/.
>
> 1) The first step is to set the variable SUBJECTS_DIR to point to
> where your subject is:
>
> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
>
> 2) The second step is to create a symbolic link so that the FreeSurfer
> "fsaverage" subject appears to be in your SUBJECTS_DIR
>
> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
>
> 3) The final step is to run mri_surf2surf to transform the 7 network
> atlas to your subject's native surfaces.
>
> >> mri_surf2surf --srcsubject fsaverage --trgsubject 100306_QD95CU_FS
> --hemi lh --sval-annot
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
> --tval $SUBJECTS_DIR/100306_QD95CU_FS/label/lh.Yeo2011_7Networks_N1000.annot
>
> Note that the above is only for the left hemisphere. You can replace
> all the "lh" with "rh" to transform the right hemisphere instead.
>
> Note that the above is for the 7 networks. You can replace all the "7"
> with "17" to transform the 17-network atlas instead.
>
> I hope the above is clearer. Let me know if you have other questions.
>
> --Thomas
>
> On Sat, Sep 19, 2015 at 4:16 PM, Ali Radaideh <ali.radai...@hu.edu.jo>
> wrote:
> > Also, could you please direct me in which directory I should save the new
> > atlas?
> >
> > Thanks,
> > Ali
> >
> > On Sat, Sep 19, 2015 at 9:47 AM, Thomas Yeo <ytho...@csail.mit.edu>
> wrote:
> >>
> >> Hi Ali,
> >>
> >> May I confirm that your data is T1 and not functional data? Here's
> >> what you can do to transfer the parcellation to your individual
> >> subject's surface mesh. After that you can use the usual commands to
> >> extract thickness, etc.
> >>
> >> In your shell (assuming you are using c shell)
> >>
> >> # First set variable s to be subject id
> >> >> set s = 100306_QD95CU_FS
> >>
> >> # set freesurfer environmental variable SUBJECTS_DIR to point to where
> >> the data is
> >> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
> >>
> >> # use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR
> >> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
> >>
> >> # use "-sval-annot" option to transfer annotation
> >> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
> >> >> --sval-annot
> >> >>
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
> >> >> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
> >>
> >> # use "sval" option to transfer confidence map.
> >> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval
> >> >>
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
> >> >> --tval
> $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
> >>
> >> Cheers,
> >> Thomas
> >>
> >> On Sat, Sep 19, 2015 at 3:12 PM, Ali R

Re: [Freesurfer] MRITOTAL

[Ali Radaideh]

Dear Z K,

I have put them in transfer/incoming folder. The file name is example.tar.gz

Thanks in advance,
Ali

On Tue, Sep 1, 2015 at 1:33 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote:

> Hello Ali,
>
> As you have observed, when there is an alignment failure using the
> talairach method, freesurfer reverts to the mni tool "mritotal". The mni
> tools will error out with mritotal because mritotal references
> "shellwords.pl" which no longer ships with new version of perl (starting
> around 5.14). In order to solve this error the user either needs to
> manually align the data or use an older version of perl.
>
> One possible work around is to use tkregister to manually align the
> image, such that mritotal is not run, and the rest of recon-all should
> run properly.
>
> If you can upload the data for a subject that fails to our ftp server I
> will take a look:
>
>https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>
> Let me know once you have uploaded the file.
>
> -Zeke
>
>
>
>
> On 09/01/2015 01:04 AM, Ali Radaideh wrote:
> > Thanks Bruce,
> >
> > Could you please suggest something for me t sort out this issue for
> > future projects. All PCs will have UBUNTU 14.04 and not of them was able
> > to run the 8 subjects. If I install an older version of UBUNTU then Ii
> > dont get and update and so can not install tcsh and csh.
> >
> > Today I am running subject number 5 of those who failed to run before.
> > It is running fine on that PC with UBUNTU 13.1.
> >
> > I want also to provide you with this info.
> >
> > All the 8 subjects did not pass the talairach step. and went to the
> > MRITOTAL stage where they all failed to run on any PC with UBUNTU 14.01.
> > However, when running them on the PC with UBUNTU 13.1, they also dont
> > pass the talairach stage and go to MRITOTAL and then the pass this step
> > and carry on.
> >
> > I thought this may help you figuring out the problem.
> >
> > Many thanks in advance,
> > Ali
> >
> > On Mon, Aug 31, 2015 at 10:31 AM, Bruce Fischl
> > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
> >
> > Hi Ali
> >
> > it's not that I know that the quality is fine. It might be (or not),
> > but this seems to be a perl error that doesn't have to do with
> quality
> > Bruce
> > On Mon, 31 Aug 2015, Ali Radaideh wrote:
> >
> > Dear Bruce and ​Jürgen,
> >
> > Now I see something important which may help solving the problem.
> >
> > I have 31 PCs in my lab and all of them are installed with
> > UBUNTU 14.04. 30
> > PCs were able to process all 47 subjects successfully. But
> > failed to process
> > the remaining 8 subjects. Fortunately, one PC is installed with
> > UBUNTU
> > 13.01. I managed to installed the tcsh and csh after update and
> > then run two
> > of the failed subjects so far successfully. I concluded it is the
> > installation version of UBUNTU. So 13.01 works fine but not
> 14.04.
> >
> > I tried to re-install 13.01 on another PC, and I did that
> > successfully.
> > However, but when I come to install the tcsh, after update it
> > fails and it
> > says it is unable to locate the package tcsh (the reason is that
> > 13.01 has
> > not longer packages to download.
> >
> > As a summary,
> >
> > one PC with 13.01 UBUNTU is running OK (but with the tcsh
> installed)
> > another OC with 13.01 is not running because I was not able to
> > install tcsh
> > after update
> >
> > I am now think of copying the tcsh from one pc to the 13.01 PC
> > to make it
> > running but still trying.
> >
> > I think as Bruce said, it is something wrong with the
> > installation as the
> > quality is fine.
> >
> > I hope I was able to clarify the problem and hope to receive any
> > helpful
> > answer.
> >
> > Many thanks in advance
> >
> > Ali
> >
> >
> >
> > On Sun, Aug 30, 2015 at 4:05 PM, Bruce Fischl
> > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>
> > wrote:
> >Hi
> > ​​Jürgen and Ali
> >
> > I don't think it has anything t

Re: [Freesurfer] MRITOTAL

[Ali Radaideh]

Thanks Bruce,

Could you please suggest something for me t sort out this issue for future
projects. All PCs will have UBUNTU 14.04 and not of them was able to run
the 8 subjects. If I install an older version of UBUNTU then Ii dont get
and update and so can not install tcsh and csh.

Today I am running subject number 5 of those who failed to run before. It
is running fine on that PC with UBUNTU 13.1.

I want also to provide you with this info.

All the 8 subjects did not pass the talairach step. and went to the
MRITOTAL stage where they all failed to run on any PC with UBUNTU 14.01.
However, when running them on the PC with UBUNTU 13.1, they also dont pass
the talairach stage and go to MRITOTAL and then the pass this step and
carry on.

I thought this may help you figuring out the problem.

Many thanks in advance,
Ali

On Mon, Aug 31, 2015 at 10:31 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Ali
>
> it's not that I know that the quality is fine. It might be (or not), but
> this seems to be a perl error that doesn't have to do with quality
> Bruce
> On Mon, 31 Aug 2015, Ali Radaideh wrote:
>
> Dear Bruce and ​Jürgen,
>>
>> Now I see something important which may help solving the problem.
>>
>> I have 31 PCs in my lab and all of them are installed with UBUNTU 14.04.
>> 30
>> PCs were able to process all 47 subjects successfully. But failed to
>> process
>> the remaining 8 subjects. Fortunately, one PC is installed with UBUNTU
>> 13.01. I managed to installed the tcsh and csh after update and then run
>> two
>> of the failed subjects so far successfully. I concluded it is the
>> installation version of UBUNTU. So 13.01 works fine but not 14.04.
>>
>> I tried to re-install 13.01 on another PC, and I did that successfully.
>> However, but when I come to install the tcsh, after update it fails and it
>> says it is unable to locate the package tcsh (the reason is that 13.01 has
>> not longer packages to download.
>>
>> As a summary,
>>
>> one PC with 13.01 UBUNTU is running OK (but with the tcsh installed)
>> another OC with 13.01 is not running because I was not able to install
>> tcsh
>> after update
>>
>> I am now think of copying the tcsh from one pc to the 13.01 PC to make it
>> running but still trying.
>>
>> I think as Bruce said, it is something wrong with the installation as the
>> quality is fine.
>>
>> I hope I was able to clarify the problem and hope to receive any helpful
>> answer.
>>
>> Many thanks in advance
>>
>> Ali
>>
>>
>>
>> On Sun, Aug 30, 2015 at 4:05 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu
>> >
>> wrote:
>>   Hi
>> ​​Jürgen and Ali
>>
>> I don't think it has anything to do with the quality of the data, but
>> we are also happy to take a look if you upload one subject. This seems
>> more like an installation issue, and I would think it would happen on
>> every subject. Did someone upgrade perl at somepoint? Or just some
>> paths?
>>
>>
>> cheers
>> Bruce
>>
>> On Sun, 30 Aug 2015, Jürgen Hänggi wrote:
>>
>>   Dear Ali
>>
>>   instead of downgrading perl you can use the perlbrew tool
>>   that allow to
>>   install several perls in parallel and switch between perl
>>   versions.
>>   if you are able to install perl 5.12 (perlbrew install
>>   5.12, you can see the
>>   available perl versions with perlbrew available) and then
>>   use
>>   perlbrew use 5.12 before running recon-all in the
>>   terminal.
>>
>>   Does it work?
>>
>>   Cheers
>>   Jürgen
>>
>>
>>
>> ---
>>
>>   Jürgen Hänggi, Ph.D.
>>
>>   Division Neuropsychology
>>
>>   Institute of Psychology
>>
>>   University of Zurich
>>
>>   Binzmuehlestrasse 14, PO Box 25
>>
>>   8050 Zurich, Switzerland
>>
>>   0041 44 635 73 97 (phone office)
>>
>>   0041 76 445 86 84 (phone mobile)
>>
>>   0041 44 635 74 09 (fax office)
>>
>>   BIN 4.D.04 (office room number)
>>
>>   j.haenggi[at]psychologie.uzh.ch (email)
>>
>>   http://www.psychologie.uzh.ch/neuropsy/ (website)
>>
>>   http://www.juergenhaenggi.ch (private website)
>>
>>
>>   This e-mail (and any attachment/s) contains confidential
>>
>>   and/or privileged information. If you are not the i

Re: [Freesurfer] MRITOTAL

[Ali Radaideh]

Dear Bruce and ​Jürgen,

Now I see something important which may help solving the problem.

I have 31 PCs in my lab and all of them are installed with UBUNTU 14.04. 30
PCs were able to process all 47 subjects successfully. But failed to
process the remaining 8 subjects. Fortunately, one PC is installed with
UBUNTU 13.01. I managed to installed the tcsh and csh after update and then
run two of the failed subjects so far successfully. I concluded it is the
installation version of UBUNTU. So 13.01 works fine but not 14.04.

I tried to re-install 13.01 on another PC, and I did that successfully.
However, but when I come to install the tcsh, after update it fails and it
says it is unable to locate the package tcsh (the reason is that 13.01 has
not longer packages to download.

As a summary,

one PC with 13.01 UBUNTU is running OK (but with the tcsh installed)
another OC with 13.01 is not running because I was not able to install tcsh
after update

I am now think of copying the tcsh from one pc to the 13.01 PC to make it
running but still trying.

I think as Bruce said, it is something wrong with the installation as the
quality is fine.

I hope I was able to clarify the problem and hope to receive any helpful
answer.

Many thanks in advance

Ali



On Sun, Aug 30, 2015 at 4:05 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi
> ​​
> Jürgen and Ali
>
> I don't think it has anything to do with the quality of the data, but we
> are also happy to take a look if you upload one subject. This seems more
> like an installation issue, and I would think it would happen on every
> subject. Did someone upgrade perl at somepoint? Or just some paths?
>
>
> cheers
> Bruce
>
> On Sun, 30 Aug 2015, Jürgen Hänggi wrote:
>
> Dear Ali
>>
>> instead of downgrading perl you can use the perlbrew tool that allow to
>> install several perls in parallel and switch between perl versions.
>> if you are able to install perl 5.12 (perlbrew install 5.12, you can see
>> the
>> available perl versions with perlbrew available) and then use
>> perlbrew use 5.12 before running recon-all in the terminal.
>>
>> Does it work?
>>
>> Cheers
>> Jürgen
>>
>>
>>
>> ---
>> Jürgen Hänggi, Ph.D.
>>
>> Division Neuropsychology
>>
>> Institute of Psychology
>>
>> University of Zurich
>>
>> Binzmuehlestrasse 14, PO Box 25
>>
>> 8050 Zurich, Switzerland
>>
>> 0041 44 635 73 97 (phone office)
>>
>> 0041 76 445 86 84 (phone mobile)
>>
>> 0041 44 635 74 09 (fax office)
>>
>> BIN 4.D.04 (office room number)
>>
>> j.haenggi[at]psychologie.uzh.ch (email)
>>
>> http://www.psychologie.uzh.ch/neuropsy/ (website)
>>
>> http://www.juergenhaenggi.ch (private website)
>>
>>
>> This e-mail (and any attachment/s) contains confidential
>>
>> and/or privileged information. If you are not the intended
>>
>> recipient (or have received this e-mail in error) please notify
>>
>> the sender immediately and destroy this e-mail. Any
>>
>> unauthorised copying, disclosure or distribution of the
>>
>> material in this e-mail is strictly forbidden.
>>
>>
>> ---
>>
>>
>>
>> Von: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ali Radaideh
>> <ali.radai...@hu.edu.jo>
>> Antworten an: Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu>
>> Datum: Samstag, 29. August 2015 15:56
>> An: Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu>
>> Betreff: Re: [Freesurfer] MRITOTAL
>>
>>   Dear Jürgen,
>>
>> Thanks for your reply. Could you please guide me on how to downgrade
>> it? I need to try everything with these 8 subjects to finish the whole
>> cohort of subjects.
>>
>> Your help is so appreciated.
>>
>> Thanks,
>> Ali
>>
>> On Sat, Aug 29, 2015 at 4:16 PM, Jürgen Hänggi
>> <j.haen...@psychologie.uzh.ch> wrote:
>>   Dear Ali
>>
>>
>> if Talairach alignment is not of good quality, then mritotal is
>> used and the shellwords.pl problem is related to the fact that
>> you have a newer version of perl that no longer contain
>> shellwords.pl.
>>
>> you can downgrade perl to 5.12 or so, which however, is not a
>> good idea.
>>
>>
>> I have no other solution
>>
>>
>> Cheers
>>
>> Jürgen
>>
>>
>>
>> Von: <freesurfer-boun...@nmr.mgh.harvard.e

Re: [Freesurfer] MRITOTAL

[Ali Radaideh]

Dear Jürgen,

Thanks for your reply. Could you please guide me on how to downgrade it? I
need to try everything with these 8 subjects to finish the whole cohort of
subjects.

Your help is so appreciated.

Thanks,
Ali

On Sat, Aug 29, 2015 at 4:16 PM, Jürgen Hänggi j.haen...@psychologie.uzh.ch
 wrote:

 Dear Ali


 if Talairach alignment is not of good quality, then mritotal is used and
 the shellwords.pl problem is related to the fact that you have a newer
 version of perl that no longer contain shellwords.pl.

 you can downgrade perl to 5.12 or so, which however, is not a good idea.


 I have no other solution


 Cheers

 Jürgen



 Von: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Ali Radaideh 
 ali.radai...@hu.edu.jo
 Antworten an: Freesurfer Mailinglist freesurfer@nmr.mgh.harvard.edu
 Datum: Samstag, 29. August 2015 13:41
 An: Freesurfer Mailinglist freesurfer@nmr.mgh.harvard.edu
 Betreff: [Freesurfer] MRITOTAL

 Dear FreeSurfer experts,

 I have sent email 10 days ago asking for a help with processing 8 out of
 55 subjects who failed to pass the Talairach phase and gave me the
 following error:

 tmpdir is transforms/tmp.talairach.5272

 /media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FILES/MS_patients/freesurfer_test/Images_test/Samer/mri
 mri_convert orig_nu.mgz transforms/tmp.talairach.5272/src.mnc
 mri_convert orig_nu.mgz transforms/tmp.talairach.5272/src.mnc
 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
 reading from orig_nu.mgz...
 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
 i_ras = (-1, 0, 0)
 j_ras = (0, 0, -1)
 k_ras = (0, 1, 0)
 writing to transforms/tmp.talairach.5272/src.mnc...
 
 mritotal -verbose -debug -clobber -modeldir
 /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm
 transforms/tmp.talairach.5272/src.mnc transforms/talairach.auto.xfm
 Can't locate shellwords.pl in @INC (@INC contains:
 /usr/local/freesurfer/mni/bin/../lib/mni_autoreg
 /usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl
 /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5
 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18
 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/mritotal line
 460.
 ERROR: mritotal failed, see transforms/talairach.log
 Linux ali-XPS-L501X 3.19.0-27-generic #29~14.04.1-Ubuntu SMP Sun Aug 16
 01:51:13 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

 recon-all -s Samer exited with ERRORS at Sat Aug 29 07:27:06 EDT 2015

 For more details, see the log file
 /media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FILES/MS_patients/freesurfer_test/Images_test/Samer/scripts/recon-all.log
 To report a problem, see
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


 Please, is there any way I can force this phase to run? I have checked the
 images and they look fine but I dont know why they failed.

 Please your response is so important to my project as everything is
 pending.

 Many thanks in advance

 Ali

 --







 *Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
 the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
 JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
 ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
 *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
 http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*

 ___ 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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 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.




-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM

[Freesurfer] MRITOTAL

[Ali Radaideh]

Dear FreeSurfer experts,

I have sent email 10 days ago asking for a help with processing 8 out of 55
subjects who failed to pass the Talairach phase and gave me the following
error:

tmpdir is transforms/tmp.talairach.5272
/media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FILES/MS_patients/freesurfer_test/Images_test/Samer/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.5272/src.mnc
mri_convert orig_nu.mgz transforms/tmp.talairach.5272/src.mnc
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig_nu.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to transforms/tmp.talairach.5272/src.mnc...

mritotal -verbose -debug -clobber -modeldir
/usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm
transforms/tmp.talairach.5272/src.mnc transforms/talairach.auto.xfm
Can't locate shellwords.pl in @INC (@INC contains:
/usr/local/freesurfer/mni/bin/../lib/mni_autoreg
/usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl
/usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18
/usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/mritotal line
460.
ERROR: mritotal failed, see transforms/talairach.log
Linux ali-XPS-L501X 3.19.0-27-generic #29~14.04.1-Ubuntu SMP Sun Aug 16
01:51:13 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s Samer exited with ERRORS at Sat Aug 29 07:27:06 EDT 2015

For more details, see the log file
/media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FILES/MS_patients/freesurfer_test/Images_test/Samer/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Please, is there any way I can force this phase to run? I have checked the
images and they look fine but I dont know why they failed.

Please your response is so important to my project as everything is pending.

Many thanks in advance

Ali

-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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Re: [Freesurfer] mritotal

[Ali Radaideh]

Hi ​Pınar,

Open a terminal
change directory to where you have saved you T1 image
type setenv SUBJECTS_DIR ${PWD}
then start you processing as follows:

Step One:
recon-all -i  (name of T1 image with its extension) -s (name of the subject)

example
recon-all -i MPRAGE.img -s Ali


Step two:
recon-all -motioncor -s Ali

Step Three:
recon-all -autorecon-all -s Ali

Hope this helps

Ali

On Mon, Aug 24, 2015 at 10:35 AM,
​​
pınar karadayı pnrkarad...@hotmail.com wrote:

 Hi Ali,
 I am also have same subject with you I am a question for you, How van I
 get recon-all for subject, please help me
 Thanks a lot
 Pınar Karadayı

 iPhone'umdan gönderildi

 23 Ağu 2015 tarihinde 19:42 saatinde, Ali Radaideh ali.radai...@hu.edu.jo
 şunları yazdı:

 Dear Freesurfer Experts,

 I have finished the recon-all for 30 subjects successfully. However, I
 started to get the following error for the remaining subjects (8 subjects)

 ​mritotal -verbose -debug -clobber -modeldir
 /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm
 transforms/tmp.talairach.6692/src.mnc transforms/talairach.auto.xfm
 Can't locate shellwords.pl in @INC (@INC contains:
 /usr/local/freesurfer/mni/bin/../lib/mni_autoreg
 /usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl
 /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5
 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18
 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/mritotal
 line 460.
 ERROR: mritotal failed, see transforms/talairach.log
 Linux imaging-ThinkCentre-16 3.13.0-40-generic #69-Ubuntu SMP Thu Nov 13
 17:53:56 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

 recon-all -s Hasan exited with ERRORS at Sun Aug 23 16:27:27 EEST 2015

 For more details, see the log file /home/imaging/processing/
 freesurfer/subjects/14-HASAN_SALAMA/Hasan/scripts/recon-all.log
 To report a problem, see
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


 ​Any ideas please. I am in urgent need to process these 8 subjects.

 Thanks in advance,
 Ali​

 --







 *Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
 the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
 JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
 ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
 *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
 http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*

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 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
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 is
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 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
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 properly
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-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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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.

[Freesurfer] mritotal

[Ali Radaideh]

Dear Freesurfer Experts,

I have finished the recon-all for 30 subjects successfully. However, I
started to get the following error for the remaining subjects (8 subjects)

​mritotal -verbose -debug -clobber -modeldir
/usr/local/freesurfer/mni/bin/../share/mni_autoreg
-protocol icbm transforms/tmp.talairach.6692/src.mnc
transforms/talairach.auto.xfm
Can't locate shellwords.pl in @INC (@INC contains:
/usr/local/freesurfer/mni/bin/../lib/mni_autoreg
/usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl
/usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18
/usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/mritotal line
460.
ERROR: mritotal failed, see transforms/talairach.log
Linux imaging-ThinkCentre-16 3.13.0-40-generic #69-Ubuntu SMP Thu Nov 13
17:53:56 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s Hasan exited with ERRORS at Sun Aug 23 16:27:27 EEST 2015

For more details, see the log file /home/imaging/processing/
freesurfer/subjects/14-HASAN_SALAMA/Hasan/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


​Any ideas please. I am in urgent need to process these 8 subjects.

Thanks in advance,
Ali​

-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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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] permission denied

[Ali Radaideh]

Hi Z K,

Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one
installed with the latest freesurfer version did not work while others
finished the processing in a reasonable processing time and I got the
results.

Also, I have a PC at my office installed with the latest freesurfer version
and it works fine. So I have two PCs installed with the latest Freesurfer
(one of them which does not work is in the lab).


To summarize:
All PCs (16 PCs in the lab and 1 in my office) are installed with latest
Ubuntu version 14.04 64 bits
15 PCs in the lab are installed with freesurfer 5.0.0 version
1 PC in the lab is installed with the latest freesurfer version (does not
work, permission denied)
1 PC in my office is installed with the latest freesurfer version (works
fine)

All these PCs have Ubuntu 14.04 64bit installed on them.



No, I am not using any vitual machine.

Regarding the root user, I will try it on Sunday as I am away for a couple
of days.

Many thanks for your continuous support.

Ali




On Thu, Oct 30, 2014 at 6:34 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:

 Ali,

 First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are
 working properly? I am under the impression that versions of freesurfer
 pre-version 5.3 will not work on newer linux distributions?


 In regards to your current permision denied issue... What happens if you
 try and run tkmedit as root user? Also, you not using virtual machine
 setup are you?

 -Zeke

 On 10/30/2014 06:27 AM, Ali Radaideh wrote:
  It does not work. This is really strange
 
  On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu
  mailto:zkauf...@nmr.mgh.harvard.edu wrote:
 
  I beleive it should have a lower case X, as in:
 
  chmod -R a+x freesurfer/bin
 
  -Zeke
 
  On 10/28/2014 01:19 AM, Ali Radaideh wrote:
Dear Douglas
   
Thanks for your reply. unfortunatey I still get the same error.
  Here is
the terminal output. Is there anything else I can do?
   
 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl
imaging@imaging-ThinkCentre-23:~$ tcsh
imaging-ThinkCentre-23:~ tkmedit
/usr/local/freesurfer/bin/tkmedit: Permission denied.
imaging-ThinkCentre-23:~
   
   
On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu wrote:
   
   
Try chmod -R a+X freesurfer/bin
   
   
On 10/26/14 1:57 PM, Ali Radaideh wrote:
Dear FreeSurfer users,
   
I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One
  of the
PCs has the latest version of freesurfer 5.3.0 while the
 others
have the version 5.0.0. The PC that is installed with the
 latest
version freesurfer 5.3.0 does not allow me to run any
  command and
everytime I try a command such such as tkmedit i get the
  following
error
/usr/local/freesurfer/bin/tkmedit: permission denied.
   
I have tried to change the permission settings
sudo chown -R imaging:imaging freesurfer
   
but did not work.
   
Any ideas why is this happening although I have done the same
thing to other PCs and they are working fine.
   
​Thanks in advance,
Ali​
   
--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo
  mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  mailto:ali.radai...@hu.edu.jo
/
/webpage:
 http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
   
   
   
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Re: [Freesurfer] permission denied

[Ali Radaideh]

It does not work. This is really strange

On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote:

 I beleive it should have a lower case X, as in:

 chmod -R a+x freesurfer/bin

 -Zeke

 On 10/28/2014 01:19 AM, Ali Radaideh wrote:
  Dear Douglas
 
  Thanks for your reply. unfortunatey I still get the same error. Here is
  the terminal output. Is there anything else I can do?
 
   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
  Setting up environment for FreeSurfer/FS-FAST (and FSL)
  FREESURFER_HOME   /usr/local/freesurfer
  FSFAST_HOME   /usr/local/freesurfer/fsfast
  FSF_OUTPUT_FORMAT nii.gz
  SUBJECTS_DIR  /usr/local/freesurfer/subjects
  MNI_DIR   /usr/local/freesurfer/mni
  FSL_DIR   /usr/local/fsl
  imaging@imaging-ThinkCentre-23:~$ tcsh
  imaging-ThinkCentre-23:~ tkmedit
  /usr/local/freesurfer/bin/tkmedit: Permission denied.
  imaging-ThinkCentre-23:~
 
 
  On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
  gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
  Try chmod -R a+X freesurfer/bin
 
 
  On 10/26/14 1:57 PM, Ali Radaideh wrote:
  Dear FreeSurfer users,
 
  I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the
  PCs has the latest version of freesurfer 5.3.0 while the others
  have the version 5.0.0. The PC that is installed with the latest
  version freesurfer 5.3.0 does not allow me to run any command and
  everytime I try a command such such as tkmedit i get the following
  error
  /usr/local/freesurfer/bin/tkmedit: permission denied.
 
  I have tried to change the permission settings
  sudo chown -R imaging:imaging freesurfer
 
  but did not work.
 
  Any ideas why is this happening although I have done the same
  thing to other PCs and they are working fine.
 
  ​Thanks in advance,
  Ali​
 
  --
  /Ali M. Al-Radaideh. PhD
  Assistant Professor
  Head of Department of Medical Imaging
  Vice Dean of the Faculty of Allied Health Sciences
  The Hashemite University,
  Zarqa, Jordan
  W.phone +962 5 390 ext.5422, 5355, 5364
  Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  /
  /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
 
 
 
  ___
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 Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
  ___
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 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.
 
 
 
 
  --
  /Ali M. Al-Radaideh. PhD
  Assistant Professor
  Head of Department of Medical Imaging
  Vice Dean of the Faculty of Allied Health Sciences
  The Hashemite University,
  Zarqa, Jordan
  W.phone +962 5 390 ext.5422, 5355, 5364
  Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  /
  /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
 
 
 
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-- 








*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical
ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite
University, Zarqa, JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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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] permission denied

[Ali Radaideh]

Dear Douglas

Thanks for your reply. unfortunatey I still get the same error. Here is the
terminal output. Is there anything else I can do?

 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl
imaging@imaging-ThinkCentre-23:~$ tcsh
imaging-ThinkCentre-23:~ tkmedit
/usr/local/freesurfer/bin/tkmedit: Permission denied.
imaging-ThinkCentre-23:~


On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:


 Try chmod -R a+X freesurfer/bin


 On 10/26/14 1:57 PM, Ali Radaideh wrote:

  Dear FreeSurfer users,

  I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs
 has the latest version of freesurfer 5.3.0 while the others have the
 version 5.0.0. The PC that is installed with the latest version freesurfer
 5.3.0 does not allow me to run any command and everytime I try a command
 such such as tkmedit i get the following error
 /usr/local/freesurfer/bin/tkmedit: permission denied.

  I have tried to change the permission settings
 sudo chown -R imaging:imaging freesurfer

  but did not work.

  Any ideas why is this happening although I have done the same thing to
 other PCs and they are working fine.

  ​Thanks in advance,
 Ali​

  --








 *Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical
 Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite
 University,  Zarqa, Jordan W.phone +962 5 390 ext.5422, 5355, 5364
 Email: ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo *
 *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
 http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*



 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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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.




-- 








*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical
ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite
University, Zarqa, JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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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] permission denied

[Ali Radaideh]

Dear FreeSurfer users,

I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has
the latest version of freesurfer 5.3.0 while the others have the version
5.0.0. The PC that is installed with the latest version freesurfer 5.3.0
does not allow me to run any command and everytime I try a command such
such as tkmedit i get the following error
/usr/local/freesurfer/bin/tkmedit: permission denied.

I have tried to change the permission settings
sudo chown -R imaging:imaging freesurfer

but did not work.

Any ideas why is this happening although I have done the same thing to
other PCs and they are working fine.

​Thanks in advance,
Ali​

-- 








*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical
ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite
University, Zarqa, JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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[Freesurfer] tkmedit_error

[Ali Radaideh]

Dear FreeSurfer experts,

I have a problem running any command in the terminal (Ubuntu 12.04). For
example when I run the following command

tkmedit bert orig.mgz

I get the following error

ERROR: A segfault has occurred. This is not your fault, : but is most
likely an unrecoverable error and has : made the program unstable. : :
Please send the contents of the file .xdebug tkmedit : that should be in
this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting...


​So I need your help please.

Ali​

-- 








*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical
ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite
University, Zarqa, JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] tkmedit

[Ali Radaideh]

Dear Don,

Thanks alot for the attachment. I have installed it as recommended and
tried the following and I started to get the error message below

imaging@imaging-ThinkCentre-20:~$ freeview
bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: bad interpreter:
Permission denied



​When using sudo before the above command and entering the password​ i get
the following message:

imaging@imaging-ThinkCentre-20:~$ sudo tkmedit -f
$FREESURFER_HOME/subjects/sample-001.mgz
sudo: tkmedit: command not found


Any idea???

On Tue, Aug 19, 2014 at 4:26 PM, Krieger, Donald N. krieg...@upmc.edu
wrote:

  Hi Ali,



 You are missing the  tcsh interpreter.

 It should be located at /bin/tcsh typically.



 It usually comes with the operating system but may not have been installed
 or may be in the wrong place for freesurfer to find it.



 I’ve attached a 64 bit i86 version which is from my installation of Fedora
 Linus.



 Regards,



 Don



 Don Krieger, Ph.D.

 Department of Neurological Surgery

 University of Pittsburgh

 (412)648-9654 Office

 (412)521-4431 Cell/Text



 *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
 freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Ali Radaideh
 *Sent:* Tuesday, August 19, 2014 8:06 AM
 *To:* Freesurfer support list
 *Subject:* Re: [Freesurfer] tkmedit



 Thanks ZK,

 I got the following message:
 bash: /usr/local/freesurfer/bin/tkmedit: /bin/tcsh: bad interpreter: No
 such file or directory



 On Tue, Aug 12, 2014 at 5:29 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:

 Ali,

 I have not encountered this issue before. Could you please provide a
 screencapture or copy/paste of the terminal output when you type:

 $ tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz

 -Zeke




 On 08/12/2014 06:48 AM, Ali Radaideh wrote:
  Dear Zeke,
 
  Thanks for your email. For some reasons your email went to the spam
 folder
 
  The build-stamps.txt file contents:
 
  freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
 
   freeview does not work
 
  Thanks,
  Ali
 
 
 
 
  On Tue, Aug 5, 2014 at 11:44 PM, Z K zkauf...@nmr.mgh.harvard.edu
  mailto:zkauf...@nmr.mgh.harvard.edu wrote:
 
  Just so its clear.. You have installed FreeSurfer on 15 Linux
 machines
  running Ubuntu? If so, can you please provide me with the contents of
  the build-stamps.txt file in the FREESURFER_HOME directory?
 
  Also, could you please inform me if freeview works by simply typing
 the
  freeview command?
 
  $ freeview
 
  -Zeke
 
 
  On 08/05/2014 04:32 PM, Ali Radaideh wrote:
Dear FreeSurfer experts,
   
I have installed FreeSurfer on multiple machines in our image
  processing
lab (15 PC, Linux Ubuntu) and made sure that the setting are fine.
However, I have tried to test if freesurfer works or not by
  typing the
following:
   
tkmedit bert orig.mgz
   
   
Unfortunately, I have got the following error message on all PCs
   
A segfault has occurred. This is not your fault,
   : but is most likely an unrecoverable error and has
   : made the program unstable.
   
   
​So what would be the error​?
   
Many thanks in advance,
Ali,
   
   
--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
/
/webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
   
   
   
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 Freesurfer@nmr.mgh.harvard.edu
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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.
 
 
 
 
  --
  /Ali M. Al-Radaideh. PhD
  Assistant Professor
  Head of Department of Medical Imaging
  Vice Dean of the Faculty of Allied Health Sciences
  The Hashemite University,
  Zarqa, Jordan
  W.phone +962 5

Re: [Freesurfer] tkmedit

[Ali Radaideh]

Thanks ZK,

I got the following message:
bash: /usr/local/freesurfer/bin/tkmedit: /bin/tcsh: bad interpreter: No
such file or directory


On Tue, Aug 12, 2014 at 5:29 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:

 Ali,

 I have not encountered this issue before. Could you please provide a
 screencapture or copy/paste of the terminal output when you type:

 $ tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz

 -Zeke




 On 08/12/2014 06:48 AM, Ali Radaideh wrote:
  Dear Zeke,
 
  Thanks for your email. For some reasons your email went to the spam
 folder
 
  The build-stamps.txt file contents:
 
  freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
 
   freeview does not work
 
  Thanks,
  Ali
 
 
 
 
  On Tue, Aug 5, 2014 at 11:44 PM, Z K zkauf...@nmr.mgh.harvard.edu
  mailto:zkauf...@nmr.mgh.harvard.edu wrote:
 
  Just so its clear.. You have installed FreeSurfer on 15 Linux
 machines
  running Ubuntu? If so, can you please provide me with the contents of
  the build-stamps.txt file in the FREESURFER_HOME directory?
 
  Also, could you please inform me if freeview works by simply typing
 the
  freeview command?
 
  $ freeview
 
  -Zeke
 
 
  On 08/05/2014 04:32 PM, Ali Radaideh wrote:
Dear FreeSurfer experts,
   
I have installed FreeSurfer on multiple machines in our image
  processing
lab (15 PC, Linux Ubuntu) and made sure that the setting are fine.
However, I have tried to test if freesurfer works or not by
  typing the
following:
   
tkmedit bert orig.mgz
   
   
Unfortunately, I have got the following error message on all PCs
   
A segfault has occurred. This is not your fault,
   : but is most likely an unrecoverable error and has
   : made the program unstable.
   
   
​So what would be the error​?
   
Many thanks in advance,
Ali,
   
   
--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
/
/webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
   
   
   
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  The information in this e-mail is intended only for the person to
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  the e-mail
  contains patient information, please contact the Partners Compliance
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  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.
 
 
 
 
  --
  /Ali M. Al-Radaideh. PhD
  Assistant Professor
  Head of Department of Medical Imaging
  Vice Dean of the Faculty of Allied Health Sciences
  The Hashemite University,
  Zarqa, Jordan
  W.phone +962 5 390 ext.5422, 5355, 5364
  Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  /
  /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
 
 
 
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-- 








*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical
ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite
University, Zarqa, JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
___
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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

Re: [Freesurfer] tkmedit

[Ali Radaideh]

Dear Zeke,

Thanks for your email. For some reasons your email went to the spam folder

The build-stamps.txt file contents:

freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0

freeview does not work

Thanks,
Ali




On Tue, Aug 5, 2014 at 11:44 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:

 Just so its clear.. You have installed FreeSurfer on 15 Linux machines
 running Ubuntu? If so, can you please provide me with the contents of
 the build-stamps.txt file in the FREESURFER_HOME directory?

 Also, could you please inform me if freeview works by simply typing the
 freeview command?

 $ freeview

 -Zeke


 On 08/05/2014 04:32 PM, Ali Radaideh wrote:
  Dear FreeSurfer experts,
 
  I have installed FreeSurfer on multiple machines in our image processing
  lab (15 PC, Linux Ubuntu) and made sure that the setting are fine.
  However, I have tried to test if freesurfer works or not by typing the
  following:
 
  tkmedit bert orig.mgz
 
 
  Unfortunately, I have got the following error message on all PCs
 
  A segfault has occurred. This is not your fault,
 : but is most likely an unrecoverable error and has
 : made the program unstable.
 
 
  ​So what would be the error​?
 
  Many thanks in advance,
  Ali,
 
 
  --
  /Ali M. Al-Radaideh. PhD
  Assistant Professor
  Head of Department of Medical Imaging
  Vice Dean of the Faculty of Allied Health Sciences
  The Hashemite University,
  Zarqa, Jordan
  W.phone +962 5 390 ext.5422, 5355, 5364
  Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  /
  /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
 
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 The information in this e-mail is intended only for the person to whom it
 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.




-- 








*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical
ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite
University, Zarqa, JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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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.

[Freesurfer] tkmedit

[Ali Radaideh]

Dear FreeSurfer experts,

I have installed FreeSurfer on multiple machines in our image processing
lab (15 PC, Linux Ubuntu) and made sure that the setting are fine. However,
I have tried to test if freesurfer works or not by typing the following:

tkmedit bert orig.mgz


Unfortunately, I have got the following error message on all PCs

A segfault has occurred. This is not your fault,
  : but is most likely an unrecoverable error and has
  : made the program unstable.


​So what would be the error​?

Many thanks in advance,
Ali,


-- 








*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical
ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite
University, Zarqa, JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
___
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] control points

[Ali Radaideh]

Hi Bruce,

The control points are now saved. It looks like I need to save them at
least 3 times. I think tkmedit interface does not respond from the first
time.

Many thanks 
Ali

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Tuesday, September 07, 2010 2:22 AM
To: Ali Radaideh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] control points

you need to visualize it in tkmedit. As for the control points, we 
haven't seen that happen. Can you try saving a couple and seeing if the 
file changes?

cheers
Bruce
On Tue, 7 Sep 2010, Ali Radaideh wrote:

 Hi Bruce

 That is strange. I have just repeated adding control points and save
 them in tkmedit (filesave control points) but when I cat the
 control.dat it shows nothing as before.

 Regarding talairach.xfm,

 MNI Transform File
 % tkregister2

 Transform_Type = Linear;
 Linear_Transform =
   1.089229940.00106384   -0.033154302.06818056
   0.050278381.18083215   -0.06254977  -14.10989380
   0.06858014   -0.252017711.33514297  -10.44485474 ;

 Does this look ok?

 Ali

 -Original Message-
 From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 07, 2010 1:30 AM
 To: Ali Radaideh
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] control points

 Hi Ali,

 that means that there are 0 control points stored in the file. For the
 2nd
 error have you checked the talairach.xfm?

 cheers
 Bruce

 On Tue, 7 Sep
 2010, Ali Radaideh wrote:

 Hi Bruce,

 Catting the file shows something like

 cat control.dat
 info
 numpoints 0
 useRealRAS 0



 The version of freesurfer is

 freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0




 Unfortunately, I repeated hat you suggested in your previous email
 (-make all) to another subject but failed at some point although this
 subject's data have been proceed month ago successfully ( the data
 from
 the first subject still running), the error is:

  second estimation of the COG coord: x=129,y=120, z=120, r=9758
 iterations
   GLOBAL  CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 22554
  RIGHT_CERCSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1548
  LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 1656
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=9, CSF_MAX=33 , nb = 9459
 LEFT_BRAINCSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 9819
OTHER  CSF_MIN=0, CSF_intensity=18, CSF_MAX=39 , nb = 72
 mri_watershed Error:
 GLOBAL region of the brain empty !
 Linux comp13 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC
 x86_64
 x86_64 x86_64 GNU/Linu
 x

 recon-all exited with ERRORS at Mon Sep  6 15:03:10 BST 2010


 Thanks
 Ali





 -Original Message-
 From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
 Sent: Monday, September 06, 2010 3:30 PM
 To: Ali Radaideh
 Subject: RE: [Freesurfer] control points

 Hi Ali,

 can you post your responses to the list? Try catting that file to see
 what's in it. Also, what version are you running?

 cheers
 Bruce


 On Mon, 6 Sep 2010, Ali Radaideh
 wrote:

 Hi Bruce,

 control.dat file is there (size=75).

 Actually I finished running this subject before and checked that.

 Now I am running the recon-all with -make all flag as you suggested
 and
 it is working fine.

 But not sure if 'reading 0 control points' means that there will be
 no
 improvement after running the recon-all !!

 Thanks
 Ali


 -Original Message-
 From: freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
 Fischl
 Sent: Monday, September 06, 2010 2:03 PM
 To: Ali Radaideh
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] control points

 Hi Ali,

 the control points are saved in the subject's directory under

 subject id/tmp/control.dat

 does that file exist? It also looks like you hadn't finished running
 this
 subject previously. Try running -make all in recon-alll which will
 rerun

 only what it needs to.

 cheers
 Bruce


 On Mon, 6 Sep
 2010, Ali Radaideh wrote:

 Dear Freesurfer experts,



 One more question for today please. I have edited the wm in tkmedit
 and
 saved the control points then ran



 Recon-all -autorecon2-cp -autorecon3 -s mySubjectName



 But unfortunately I got the following message after 5min of
running.
 I
 tried to use a different subject but I got the same message again.



 It was displaying a message that it is 'reading 0 control points'.
 Is
 this message related to the error below?



 mri_fill -a ../scripts/ponscc.cut.log -xform
 transforms/talairach.lta
 -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz



 logging cutting plane coordinates to ../scripts/ponscc.cut.log...

 INFO: Using transforms/talairach.lta and its offset for Talairach
 volume
 ...

 using segmentation aseg.auto_noCCseg.mgz...

 reading input volume...done.

 searching for cutting planes...voxel to talairach voxel transform

 1.047   0.006   0.067  -14.718;

 0.005   1.161   0.015  -27.233

[Freesurfer] control points

[Ali Radaideh]

Dear Freesurfer experts,

 

One more question for today please. I have edited the wm in tkmedit and
saved the control points then ran

 

Recon-all -autorecon2-cp -autorecon3 -s mySubjectName

 

But unfortunately I got the following message after 5min of running. I
tried to use a different subject but I got the same message again.

 

It was displaying a message that it is 'reading 0 control points'. Is
this message related to the error below?

 

mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
-segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz

 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...

INFO: Using transforms/talairach.lta and its offset for Talairach volume
...

using segmentation aseg.auto_noCCseg.mgz...

reading input volume...done.

searching for cutting planes...voxel to talairach voxel transform

 1.047   0.006   0.067  -14.718;

 0.005   1.161   0.015  -27.233;

-0.083  -0.006   1.022  -2.059;

 0.000   0.000   0.000   1.000;

mri_fill: could not read segmentation from aseg.auto_noCCseg.mgz

reading segmented volume aseg.auto_noCCseg.mgz...

ERROR: cannot find
/data_local/ali/freesurfer/subjects/ali1/mri/aseg.auto_noCCseg.mgz

No such file or directory

Linux comp07 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC x86_64
x86_64 x86_64 GNU   /Linux

 

recon-all exited with ERRORS at Mon Sep  6 13:00:12 BST 2010

 

 

 

Many thanks

Ali

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Re: [Freesurfer] control points

[Ali Radaideh]

Hi Bruce,

Catting the file shows something like

cat control.dat
info
numpoints 0
useRealRAS 0



The version of freesurfer is

freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0




Unfortunately, I repeated hat you suggested in your previous email
(-make all) to another subject but failed at some point although this
subject's data have been proceed month ago successfully ( the data from
the first subject still running), the error is:

  second estimation of the COG coord: x=129,y=120, z=120, r=9758
iterations
   GLOBAL  CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 22554
  RIGHT_CERCSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1548
  LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 1656
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=9, CSF_MAX=33 , nb = 9459
 LEFT_BRAINCSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 9819
OTHER  CSF_MIN=0, CSF_intensity=18, CSF_MAX=39 , nb = 72
mri_watershed Error:
 GLOBAL region of the brain empty !
Linux comp13 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC x86_64
x86_64 x86_64 GNU/Linu
x

recon-all exited with ERRORS at Mon Sep  6 15:03:10 BST 2010


Thanks
Ali





-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Monday, September 06, 2010 3:30 PM
To: Ali Radaideh
Subject: RE: [Freesurfer] control points

Hi Ali,

can you post your responses to the list? Try catting that file to see 
what's in it. Also, what version are you running?

cheers
Bruce


On Mon, 6 Sep 2010, Ali Radaideh 
wrote:

 Hi Bruce,

 control.dat file is there (size=75).

 Actually I finished running this subject before and checked that.

 Now I am running the recon-all with -make all flag as you suggested
and
 it is working fine.

 But not sure if 'reading 0 control points' means that there will be no
 improvement after running the recon-all !!

 Thanks
 Ali


 -Original Message-
 From: freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
 Fischl
 Sent: Monday, September 06, 2010 2:03 PM
 To: Ali Radaideh
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] control points

 Hi Ali,

 the control points are saved in the subject's directory under

 subject id/tmp/control.dat

 does that file exist? It also looks like you hadn't finished running
 this
 subject previously. Try running -make all in recon-alll which will
rerun

 only what it needs to.

 cheers
 Bruce


 On Mon, 6 Sep
 2010, Ali Radaideh wrote:

 Dear Freesurfer experts,



 One more question for today please. I have edited the wm in tkmedit
 and
 saved the control points then ran



 Recon-all -autorecon2-cp -autorecon3 -s mySubjectName



 But unfortunately I got the following message after 5min of running.
I
 tried to use a different subject but I got the same message again.



 It was displaying a message that it is 'reading 0 control points'. Is
 this message related to the error below?



 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
 -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz



 logging cutting plane coordinates to ../scripts/ponscc.cut.log...

 INFO: Using transforms/talairach.lta and its offset for Talairach
 volume
 ...

 using segmentation aseg.auto_noCCseg.mgz...

 reading input volume...done.

 searching for cutting planes...voxel to talairach voxel transform

 1.047   0.006   0.067  -14.718;

 0.005   1.161   0.015  -27.233;

 -0.083  -0.006   1.022  -2.059;

 0.000   0.000   0.000   1.000;

 mri_fill: could not read segmentation from aseg.auto_noCCseg.mgz

 reading segmented volume aseg.auto_noCCseg.mgz...

 ERROR: cannot find
 /data_local/ali/freesurfer/subjects/ali1/mri/aseg.auto_noCCseg.mgz

 No such file or directory

 Linux comp07 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC
 x86_64
 x86_64 x86_64 GNU   /Linux



 recon-all exited with ERRORS at Mon Sep  6 13:00:12 BST 2010







 Many thanks

 Ali

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[Freesurfer] cortical volume

[Ali Radaideh]

Hello,

 

After the success of running the freesurfer on the 7T human data a while
ago, I am trying now to extract the cortical volume. However, if I use
asegstats2table command to get the segmented volume then I get the
following values

 

Rt_cerebral_cortex = 236732

Lt_cerebral cortex = 242649

 

While if I use the read_curv  in Matlab I get the following values 

 

Rt_cerebral_cortex = 209050

Lt_cerebral cortex = 208080

 

 

Any reasons for such difference, please?

 

As I need also to normalise these values to the intracranial volume ICV,
do you think it is better then to use the asegstats2table command as it
lists the ICV in its outputs as well?

 

Many thanks in advance

 

Ali

This message and any attachment are intended solely for the addressee and may 
contain confidential information. If you have received this message in error, 
please send it back to me, and immediately delete it.   Please do not use, copy 
or disclose the information contained in this message or in any attachment.  
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dispose of the e-mail.

[Freesurfer] tkmedit and intensity normalisation

[Ali Radaideh]

Dear FreeSurfer experts,



I have two question for you please,

First, I started recently to get the following message when I try to
load the tkmedit

GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by
display: IP address

 And sometimes

tkmedit.bin: xcb_io.c:452: _XRead: Assertion `dpy-xcb-reply_data != 0'
failed. aborted

 

 

Second, I have some images that have both intensity normalisation and
Geometric distortion due to MS lesions. I followed the tutorial on how
to fix these problems. My question is that, I don't want to re-run
freesurfer twice (when I fix the intensity normalisation and one when I
edit the white matter). Is there any command line I can use after saving
changes to do both?.

 


Many thanks in advance

Ali

This message and any attachment are intended solely for the addressee and may 
contain confidential information. If you have received this message in error, 
please send it back to me, and immediately delete it.   Please do not use, copy 
or disclose the information contained in this message or in any attachment.  
Any views or opinions expressed by the author of this email do not necessarily 
reflect the views of the University of Nottingham.

This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could damage your computer system:
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dispose of the e-mail.

[Freesurfer] exited with errors

[Ali Radaideh]

Dear Freesurfer experts,

 

I was running freesurfer in a normal way as usual but unfortunately I
got the following error. This is the first time I see this error. Any
ideas, please?

 

Many thanks in advance

Ali

 

Reporting on  48 segmentations

#

#...@# Cortical ribbon mask rh Sun Oct 25 06:18:23 GMT 2009
/data_local/olivier/qCEST/study/freesurfer/subjects/subject02/mri

 

 mris_volmask --label_left_white 2 --label_left_ribbon 3
--label_right_white 41 --label_right_ribbon 42 --save_ribbon
--save_distance subject02

 

mris_volmask.bin: error while loading shared libraries: libjpeg.so.62: 

cannot open shared object file: No such file or directory Linux comp14
2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC x86_64

x86_64 x86_64 GNU/Linux

 

recon-all exited with ERRORS at Sun Oct 25 06:18:25 GMT 2009


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