segmentHA_T2.sh issue, ERROR: cannot find transform file

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Chen Guoyang (IMH)

26 Oct 2018 26 Oct '18

6:34 a.m.

External Email - Use Caution

Dear Freesurfer experts,

I am currently attempting to include an additional T2 MRI scan in the segmentation of our T1 scan. The freesurfer version that I'm using is the freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version).

However, I ran into this issue, ERROR: cannot find transform file. I've pasted the output below.

Will like your advices for the this matter.

Thanks!

Sincerely,

Guoyang

OS Darwin Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 ------------------------------

#-------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib: Registering norm.mgz to additional volume /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii.

/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz --maskmov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta gunzip: can't stat: /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz (/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz.gz): No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207)

MATLAB:badSwitchExpression Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018

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Iglesias Gonzalez, Eugenio

26 Oct 26 Oct

7:52 a.m.

New subject: segmentHA_T2.sh issue, ERROR: cannot find transform file

External Email - Use Caution

It seems like a problem with mri_robust_register. Martin, any ideas?

-- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Chen Guoyang (IMH)" Guoyang_CHEN@imh.com.sg Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 26 October 2018 at 11:35 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

External Email - Use Caution

Dear Freesurfer experts,

However, I ran into this issue, ERROR: cannot find transform file. I've pasted the output below.

Will like your advices for the this matter.

Thanks!

Sincerely,

Guoyang

OS Darwin Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 ------------------------------

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207)

MATLAB:badSwitchExpression Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018

Martin Reuter

27 Oct 27 Oct

4:59 a.m.

New subject: segmentHA_T2.sh issue, ERROR: cannot find transform file

Hi,

Looks like the input is a multi frame image. Should only be single frame.

Best Martin

...

On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio e.iglesias@ucl.ac.uk wrote:

It seems like a problem with mri_robust_register. Martin, any ideas?

-- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http://www.jeiglesias.com http://www.jeiglesias.com/

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Chen Guoyang (IMH)" Guoyang_CHEN@imh.com.sg Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 26 October 2018 at 11:35 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file
    External Email - Use Caution        
Dear Freesurfer experts,

I am currently attempting to include an additional T2 MRI scan in the segmentation of our T1 scan. The freesurfer version that I'm using is the freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version).

However, I ran into this issue, ERROR: cannot find transform file. I've pasted the output below.

Will like your advices for the this matter.

Thanks!

Sincerely,

Guoyang

OS Darwin Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64

#--------------------------------------------

#@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018

Setting up environment variables

DYLD_LIBRARY_PATH is .:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib: Registering norm.mgz to additional volume /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii.

/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz --maskmov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta gunzip: can't stat: /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz (/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz.gz): No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207)

MATLAB:badSwitchExpression Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018

Chen Guoyang (IMH)

30 Oct 30 Oct

midnight

New subject: segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}

External Email - Use Caution

Hi Martin,

Thanks for the input! It worked perfectly.

A follow up question:

I understand that for T1 hippocampal subfield segmentation, Freesurfer has a longitudinal module for it (segmentHA_T1.long.sh)

Does freesurfer have a longitudinal module for T1+T2 hippocampal segmentations?

If such a module is not available, will just like to consult you guys whether are our current processing steps appropriate for longitudinal comparisons:

1. Run the longitudinal pipeline (FSv6.0) across all our subjects and each of their timepoints, example:

recon-all -long Subject1_timepoint1 Subject1_base

recon-all -long Subject1_timepoint2 Subject1_base

2. Run segmentHA_T2.sh across each longitudinal scan of each of our subjects, example: segmentHA_T2.sh Subject1_timepoint1 Subject1_timepoint1.long.Subject1_base Subject1_timepoint1_T2.nii T2 1 segmentHA_T2.sh Subject1_timepoint2 Subject1_timepoint2.long.Subject1_base Subject1_timepoint2_T2.nii T2 1

Thanks!

Yours Sincerely, Guoyang

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter Sent: Saturday, 27 October, 2018 4:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

Hi,

Looks like the input is a multi frame image. Should only be single frame.

Best Martin

On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

It seems like a problem with mri_robust_register. Martin, any ideas?

-- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http://www.jeiglesias.com https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.jeiglesias.com&umid=03F7EE2E-7932-1105-AA91-DA9BE547B048&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-dbc6e738e10a2646a86a99f0c9e164a3bdf6af7c

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Chen Guoyang (IMH)" <Guoyang_CHEN@imh.com.sgmailto:Guoyang_CHEN@imh.com.sg> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 26 October 2018 at 11:35 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

External Email - Use Caution Dear Freesurfer experts,

However, I ran into this issue, ERROR: cannot find transform file. I've pasted the output below.

Will like your advices for the this matter.

Thanks!

Sincerely, Guoyang

OS Darwin Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 ------------------------------

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207)

MATLAB:badSwitchExpression Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018

Iglesias Gonzalez, Eugenio

3:42 a.m.

New subject: segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}

External Email - Use Caution

Hi Gouyang There's no T2 longitudinal pipeline available at the moment. In its absence, what you're doing is the way to go ;-)

Sent from my phone, please excuse brevity and typos

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Chen Guoyang (IMH) Guoyang_CHEN@imh.com.sg Sent: Tuesday, October 30, 2018 4:00:54 AM To: Freesurfer support list Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}

External Email - Use Caution Hi Martin,

Thanks for the input! It worked perfectly.

A follow up question:

I understand that for T1 hippocampal subfield segmentation, Freesurfer has a longitudinal module for it (segmentHA_T1.long.sh)

Does freesurfer have a longitudinal module for T1+T2 hippocampal segmentations?

If such a module is not available, will just like to consult you guys whether are our current processing steps appropriate for longitudinal comparisons:

1. Run the longitudinal pipeline (FSv6.0) across all our subjects and each of their timepoints, example:

recon-all –long Subject1_timepoint1 Subject1_base

recon-all –long Subject1_timepoint2 Subject1_base

Thanks!

Yours Sincerely, Guoyang

Hi,

Looks like the input is a multi frame image. Should only be single frame.

Best Martin

On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

It seems like a problem with mri_robust_register. Martin, any ideas?

-- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London MailScanner has detected a possible fraud attempt from "imsva91-ctp.trendmicro.com:443" claiming to be http://www.jeiglesias.com https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.jeiglesias.com&umid=03F7EE2E-7932-1105-AA91-DA9BE547B048&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-dbc6e738e10a2646a86a99f0c9e164a3bdf6af7c

External Email - Use Caution Dear Freesurfer experts,

However, I ran into this issue, ERROR: cannot find transform file. I've pasted the output below.

Will like your advices for the this matter.

Thanks!

Sincerely, Guoyang

OS Darwin Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 ------------------------------

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207)

MATLAB:badSwitchExpression Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018

Chen Guoyang (IMH)

4:02 a.m.

New subject: segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}

External Email - Use Caution

Hi Martin,

That was helpful! Thanks a lot =)!

Sincerely, Guoyang

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Tuesday, 30 October, 2018 3:42 PM To: Freesurfer support list; Freesurfer support list Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}

[<extmail>] <EXTMSG>

External Email - Use Caution Hi Gouyang There's no T2 longitudinal pipeline available at the moment. In its absence, what you're doing is the way to go ;-) Sent from my phone, please excuse brevity and typos

External Email - Use Caution Hi Martin,

Thanks for the input! It worked perfectly.

A follow up question:

I understand that for T1 hippocampal subfield segmentation, Freesurfer has a longitudinal module for it (segmentHA_T1.long.sh)

Does freesurfer have a longitudinal module for T1+T2 hippocampal segmentations?

If such a module is not available, will just like to consult you guys whether are our current processing steps appropriate for longitudinal comparisons:

1. Run the longitudinal pipeline (FSv6.0) across all our subjects and each of their timepoints, example:

recon-all –long Subject1_timepoint1 Subject1_base

recon-all –long Subject1_timepoint2 Subject1_base

Thanks!

Yours Sincerely, Guoyang

Hi,

Looks like the input is a multi frame image. Should only be single frame.

Best Martin

On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

It seems like a problem with mri_robust_register. Martin, any ideas?

-- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London MailScanner has detected a possible fraud attempt from "imsva91-ctp.trendmicro.com:443" claiming to be http://www.jeiglesias.com https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.jeiglesias.com&umid=71194998-796D-5C05-B267-234AD4864866&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-1eadf74d3680c0d2525f564e41aef50408f84520

External Email - Use Caution Dear Freesurfer experts,

However, I ran into this issue, ERROR: cannot find transform file. I've pasted the output below.

Will like your advices for the this matter.

Thanks!

Sincerely, Guoyang

OS Darwin Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 ------------------------------

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207)

MATLAB:badSwitchExpression Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018

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5 comments

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participants (3)

Chen Guoyang (IMH)
Iglesias Gonzalez, Eugenio
Martin Reuter