The output looks correct to me.
The functional gifti file doesn't have the vertex coordinate information. It is
like a surface overlay. It only contains one value for each vertex.
The pial and white surface gifti files have the vertex coordinates and
information about how triangles are formed.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of wangzhiwei3233
Sent: Tuesday, January 30, 2024 1:27 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] converting preprecessed functional surface data to
gifti
External Email - Use Caution
Dear Yujing,
Thank you for your response.
I attempted the command again as follows:
mris_convert -f $funcfile ${SUBJECTS_DIR}/fsaverage/surf/${hemi}.white
./$fname.gii
This time, no errors were reported. However, upon comparison, it appears that
the output gii file is identical (same file size) to the output from the
following command line:
mri_convert $funcfile ./$fname.gii (Note: mri_convert, not mris_convert)
The content of the output file is as follows:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE GIFTI SYSTEM "http://gifti.projects.nitrc.org/gifti.dtd";>
<GIFTI Version="1.0" NumberOfDataArrays="1">
<MetaData>
<MD>
<Name><![CDATA[UserName]]></Name>
<Value><![CDATA[wzw]]></Value>
</MD>
<MD>
<Name><![CDATA[Date]]></Name>
<Value><![CDATA[Tue Jan 30 11:31:22 2024]]></Value>
</MD>
<MD>
<Name><![CDATA[gifticlib-version]]></Name>
<Value><![CDATA[gifti library version 1.09, 28 June, 2010]]></Value>
</MD>
</MetaData>
<LabelTable/>
<DataArray Intent="NIFTI_INTENT_NONE"
DataType="NIFTI_TYPE_FLOAT32"
ArrayIndexingOrder="RowMajorOrder"
Dimensionality="1"
Dim0="163842"
Encoding="GZipBase64Binary"
Endian="LittleEndian"
ExternalFileName=""
ExternalFileOffset="">
<MetaData/>
<Data>eJysunV4ldfWtxsh7u7utuLua95xJ8RICQQnFA1OCQQIWjQ4xYsXdyheNDR4sKLBKSSEIkkg+Z69r+vd17fP6dnvOd975j9rZeVZz5xzzDF+4/(.....more
lines like this, not shown )
It appears that there is no vertex coordinate information in it. I am uncertain
whether the output result file is correct. What should the output file look
like?
My ultimate goal is to perform GLM analysis in SPM using these gii data. The
'gifti' function in SPM can read the output gii file, but it contains only
values (cdata: 163842×1 single), as I split the frames, so the frame is "×1".
This leads to errors in further analysis. I also converted the pial surface to
gii and read it using the 'gifti' function in SPM; it contained three fields:
faces: [327680×3 int32]
mat: [4×4 double]
vertices: [163842×3 single]
It seems that there is no problem with converting the pial surface to gii, but
there is an issue with converting functional surface data to gii.
Best,
zhiwei
Date: Fri, 26 Jan 2024 13:29:24 +0000
From: "Huang, Yujing"
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] converting preprecessed functional surface
data to gifti
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:
<mn2pr04mb5982358d1de7cf24b4127e7c9d...@mn2pr04mb5982.namprd04.prod.outlook.com<mailto:mn2pr04mb5982358d1de7cf24b4127e7c9d...@mn2pr04mb5982.namprd04.prod.outlook.com>>
Content-Type: text/plain; charset="utf-8"
How does your command line look like? To convert functional file, use ?-f
<function-file>?. You also need to specify surface file.
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of wangzhiwei3233
Sent: Friday, January 26, 2024 4:39 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] converting preprecessed functional surface data to gifti
External Email - Use Caution
Dear Freesurfer experts,
How can I convert the preprecessed functional surface data to gifti
format(gii)?
I tried mris_convert, but I encountered the following error.
error: freadFloat: fread failed
Your assistance would be highly appreciated.
Best regards,
zhiwei
_______________________________________________
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 Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
