Re: [Freesurfer] Analysing HCP Data in freesurfer
External Email - Use Caution
@Freesurfer Developers
It would be pretty great if HCP analysis was compatible and could be done
with freesurfer.
On Fri, Jul 30, 2021 at 3:15 PM Poortata Shirish Lalwani
wrote:
> Thanks Matt. That is super helpful!!
>
> On Fri, Jul 30, 2021 at 1:40 PM Glasser, Matthew
> wrote:
>
>> External Email - Use Caution
>>
>> The updated version of this pipeline is now available in the master
>> branch and will be what we will use for the official lifespan task fMRI
>> analysis.
>>
>>
>>
>> Matt.
>>
>>
>>
>> *From: * on behalf of "Glasser,
>> Matthew"
>> *Reply-To: *Freesurfer support list
>> *Date: *Friday, July 30, 2021 at 7:43 AM
>> *To: *Freesurfer support list
>> *Subject: *Re: [Freesurfer] Analysing HCP Data in freesurfer
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Like I said before, the HCP has a task analysis pipeline written
>> specifically for CIFTI (and FSL also has CIFTI enabled tools). *MailScanner
>> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
>> to be*
>> https://secure-web.cisco.com/1SEzSwB0VuGx9pd_n7SWEc3f-Tyy8mtEKvEhCuDvWPcrpsJWgUrVgiur9j2dsyrueSBXBxJclKXsZBmOu9HlHVi1oDW3jWoW8oEn2dy3vmxiPXCmJI6isb5tMEmpL9AkNhNAMfch2wSSHDxpS8uGjWYvm7UQh9R9mPKnNvhQ8bJWGcIgKPv4INRM5z9xnQY_mPcvTWcSdnwy-yvSDz3WS64m6sucbEBLQ3BOvzkxwbKiMEdCSWxmYEt19fbNpgO9PJoePOjMB-EZafE63TBpitQ/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Ftree%2Fmaster%2FTaskfMRIAnalysis
>> <https://secure-web.cisco.com/16-PqNZ69sCQhtOyBAv6e4grcj8m_fit1m4rcGKVXpOrLNVugaZo3icg0pLBSV4wtun0b4kmIikMHHHnTTJ7vO1EHem-hIoujNWBxSlJ30hgliCDTAjse7ynaaSJ0_zENeFeTnpx1U5M0vk6Vm5vHlw-UWhHaveKjv14mj99lDc67AKfXabxEuoywh3rH3XnOo8WQm_7IHtXEEeGL8raiZ76ZsLZUfbL_j1-ulO04Mzaqf3cqMwu-W8VswfCB7FzwP3a9VSoY0ToeI_pWG6_m6g/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Ftree%2Fmaster%2FTaskfMRIAnalysis>
>>
>>
>>
>> We will be merging in a new version in the next few days.
>>
>> Matt.
>>
>>
>>
>> *From: * on behalf of Poortata
>> Shirish Lalwani
>> *Reply-To: *Freesurfer support list
>> *Date: *Friday, July 30, 2021 at 7:43 AM
>> *To: *Freesurfer support list
>> *Subject: *Re: [Freesurfer] Analysing HCP Data in freesurfer
>>
>>
>>
>> *External Email - Use Caution*
>>
>> I wanted to perform event related analysis of the task fmri data but
>> create my own design file for the analysis. Also I do prefer to do it in
>> surface space.
>>
>>
>>
>> I have been able to use FSL for task fmri analysis on the unprocessed raw
>> volume file and run event related analysis on the HCP young dataset by
>> modifying the HCP pipeline. But wasn't able to find a straight forward way
>> to do so with HCP lifespan dataset using the recommended aligned files. FSL
>> can't open the dtseries.nii file so I am guessing it needs something else?
>> If you can share the code that can do glm fitting and cope estimation in
>> surface space for the lifespan data (assuming I just didn't locate it
>> right), that would be immensely helpful.
>>
>>
>>
>> Relatedly, my understanding is that this should be straightforward even
>> in freesurfer since it is simple glm fitting. I figured all the necessary
>> files are already created for the HCP data and it is just a matter of
>> renaming files and modifying the directory structure in a way Freesurfer
>> prefers. But maybe not? I am not sure what files the smoothing function is
>> looking for. I do think it would be really useful for many other users to
>> be able to work with HCP data in freesurfer. Thanks for your help in doing
>> this.
>>
>>
>>
>>
>>
>> Best,
>>
>> Pia
>>
>>
>>
>> On Thu, Jul 29, 2021, 11:48 AM Glasser, Matthew
>> wrote:
>>
>> *External Email - Use Caution*
>>
>> It might be easier to use the HCP’s TaskAnalysis Pipeline (of which there
>> will be a new version in the master development branch shortly that has
>> improvements for the HCP Lifespan projects), as that is designed to work
>> directly with the other outputs of the HCP Pipeline. It is correct that we
>> recommend starting from the cleaned and MSMAll aligned functional MRI data:
>>
>>
>>
>>
>> ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp0_clean.dtseries.nii
>>
>>
>>
>> It would be nice to support fsfast als
Re: [Freesurfer] Analysing HCP Data in freesurfer
External Email - Use Caution
Thanks Matt. That is super helpful!!
On Fri, Jul 30, 2021 at 1:40 PM Glasser, Matthew wrote:
> External Email - Use Caution
>
> The updated version of this pipeline is now available in the master branch
> and will be what we will use for the official lifespan task fMRI analysis.
>
>
>
> Matt.
>
>
>
> *From: * on behalf of "Glasser,
> Matthew"
> *Reply-To: *Freesurfer support list
> *Date: *Friday, July 30, 2021 at 7:43 AM
> *To: *Freesurfer support list
> *Subject: *Re: [Freesurfer] Analysing HCP Data in freesurfer
>
>
>
> *External Email - Use Caution*
>
> Like I said before, the HCP has a task analysis pipeline written
> specifically for CIFTI (and FSL also has CIFTI enabled tools). *MailScanner
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
> to be*
> https://secure-web.cisco.com/1pj2ei2NF_FdOi-SIkvbHBgQfYuwRk0NtWuh04jeMq4pI5Zv-R_xDghYmc2lTZ7aBwE72jBkDLBSFZLaH_8KHxciNQ23XtrHNVxJ_2WttO3DG-ONBLPtDc8o7JvGIVjRs4QW1dtsApo4fgxBkf0zHi9hfslXw9mF9poPhNM-F2krebQWkan8rv6wscUwbw4mokYv7-vqlfhXplZX4NFRp2yCvvohtUlwSf5I5t0B0lIBWubgwpsYcPwZ4407teF3aO2MIcYPLw9B4WMRRKtdD0g/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Ftree%2Fmaster%2FTaskfMRIAnalysis
> <https://secure-web.cisco.com/16-PqNZ69sCQhtOyBAv6e4grcj8m_fit1m4rcGKVXpOrLNVugaZo3icg0pLBSV4wtun0b4kmIikMHHHnTTJ7vO1EHem-hIoujNWBxSlJ30hgliCDTAjse7ynaaSJ0_zENeFeTnpx1U5M0vk6Vm5vHlw-UWhHaveKjv14mj99lDc67AKfXabxEuoywh3rH3XnOo8WQm_7IHtXEEeGL8raiZ76ZsLZUfbL_j1-ulO04Mzaqf3cqMwu-W8VswfCB7FzwP3a9VSoY0ToeI_pWG6_m6g/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Ftree%2Fmaster%2FTaskfMRIAnalysis>
>
>
>
> We will be merging in a new version in the next few days.
>
> Matt.
>
>
>
> *From: * on behalf of Poortata
> Shirish Lalwani
> *Reply-To: *Freesurfer support list
> *Date: *Friday, July 30, 2021 at 7:43 AM
> *To: *Freesurfer support list
> *Subject: *Re: [Freesurfer] Analysing HCP Data in freesurfer
>
>
>
> *External Email - Use Caution*
>
> I wanted to perform event related analysis of the task fmri data but
> create my own design file for the analysis. Also I do prefer to do it in
> surface space.
>
>
>
> I have been able to use FSL for task fmri analysis on the unprocessed raw
> volume file and run event related analysis on the HCP young dataset by
> modifying the HCP pipeline. But wasn't able to find a straight forward way
> to do so with HCP lifespan dataset using the recommended aligned files. FSL
> can't open the dtseries.nii file so I am guessing it needs something else?
> If you can share the code that can do glm fitting and cope estimation in
> surface space for the lifespan data (assuming I just didn't locate it
> right), that would be immensely helpful.
>
>
>
> Relatedly, my understanding is that this should be straightforward even in
> freesurfer since it is simple glm fitting. I figured all the necessary
> files are already created for the HCP data and it is just a matter of
> renaming files and modifying the directory structure in a way Freesurfer
> prefers. But maybe not? I am not sure what files the smoothing function is
> looking for. I do think it would be really useful for many other users to
> be able to work with HCP data in freesurfer. Thanks for your help in doing
> this.
>
>
>
>
>
> Best,
>
> Pia
>
>
>
> On Thu, Jul 29, 2021, 11:48 AM Glasser, Matthew
> wrote:
>
> *External Email - Use Caution*
>
> It might be easier to use the HCP’s TaskAnalysis Pipeline (of which there
> will be a new version in the master development branch shortly that has
> improvements for the HCP Lifespan projects), as that is designed to work
> directly with the other outputs of the HCP Pipeline. It is correct that we
> recommend starting from the cleaned and MSMAll aligned functional MRI data:
>
>
>
>
> ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp0_clean.dtseries.nii
>
>
>
> It would be nice to support fsfast also as it is a surface-based approach,
> but I don’t personally have any experience with fsfast. Thus far, the FSL
> developers have been most engaged in supporting CIFTI with their tools (and
> the HCP’s task analysis pipeline is based on FSL’s FEAT), but I would be
> happy to work with the FreeSurfer developers to figure out the best way for
> users to process CIFTI data with fsfast if there is a mutual interest in
> this.
>
>
>
> Matt.
>
>
>
> *
Re: [Freesurfer] Analysing HCP Data in freesurfer
External Email - Use Caution
I wanted to perform event related analysis of the task fmri data but create
my own design file for the analysis. Also I do prefer to do it in surface
space.
I have been able to use FSL for task fmri analysis on the unprocessed raw
volume file and run event related analysis on the HCP young dataset by
modifying the HCP pipeline. But wasn't able to find a straight forward way
to do so with HCP lifespan dataset using the recommended aligned files. FSL
can't open the dtseries.nii file so I am guessing it needs something else?
If you can share the code that can do glm fitting and cope estimation in
surface space for the lifespan data (assuming I just didn't locate it
right), that would be immensely helpful.
Relatedly, my understanding is that this should be straightforward even in
freesurfer since it is simple glm fitting. I figured all the necessary
files are already created for the HCP data and it is just a matter of
renaming files and modifying the directory structure in a way Freesurfer
prefers. But maybe not? I am not sure what files the smoothing function is
looking for. I do think it would be really useful for many other users to
be able to work with HCP data in freesurfer. Thanks for your help in doing
this.
Best,
Pia
On Thu, Jul 29, 2021, 11:48 AM Glasser, Matthew wrote:
> External Email - Use Caution
>
> It might be easier to use the HCP’s TaskAnalysis Pipeline (of which there
> will be a new version in the master development branch shortly that has
> improvements for the HCP Lifespan projects), as that is designed to work
> directly with the other outputs of the HCP Pipeline. It is correct that we
> recommend starting from the cleaned and MSMAll aligned functional MRI data:
>
>
>
>
> ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp0_clean.dtseries.nii
>
>
>
> It would be nice to support fsfast also as it is a surface-based approach,
> but I don’t personally have any experience with fsfast. Thus far, the FSL
> developers have been most engaged in supporting CIFTI with their tools (and
> the HCP’s task analysis pipeline is based on FSL’s FEAT), but I would be
> happy to work with the FreeSurfer developers to figure out the best way for
> users to process CIFTI data with fsfast if there is a mutual interest in
> this.
>
>
>
> Matt.
>
>
>
> *From: * on behalf of Poortata
> Shirish Lalwani
> *Reply-To: *Freesurfer support list
> *Date: *Thursday, July 29, 2021 at 11:39 AM
> *To: *Freesurfer support list
> *Subject: *Re: [Freesurfer] Analysing HCP Data in freesurfer
>
> *External Email - Use Caution*
>
> I am trying to analyse the HCP-Aging vismotor task fMRI data
> <https://secure-web.cisco.com/1Z30FmBulf3wPk8ZI1piszdCtNxfv_oM8hAju_21Q2rqxpYuGRsbRPC84dN3sp47oBdJLeOU7T9szqn8hcIkH4BhLhOBGhJvd5XLqntcuUFtPaWurM0LgbDUCjvps3yPQB_EvdAfv_Ao-NgAp8KZNUYyv4AybUV5-WXbC3PjGeQIaj7FgDLIVaKTIx1Snw558T4Vnz72IWqJurISu__OS0h5zc-uKdjgeB4bPhvloeUMkY57oe6VxBLQ93zhlWAyKpxdlrKxLcu1BnxApRJa6kA/https%3A%2F%2Fwww.humanconnectome.org%2Fstudy%2Fhcp-lifespan-aging%2Fproject-protocol%2Ftask-protocols-hcp-aging>
> with an event-based design. The provided file is dtseries.nii format and is
> the recommended starting point for tfMRI analyses by HCP-Aging. The cleaned
> file is precisely aligned across subjects using the MSMAll multimodal
> surface registration and is created applying
> GenericfMRIVolumeProcessingPipeline, GenericfMRISurfaceProcessingPipeline,
> hcp_fix_multi_run, and MSMAllPipeline. I was hoping to simply run GLM
> analysis on this file in fsfast but I am not sure which files the smoothing
> function is searching for since it is surface-based analysis.
>
>
>
> On Thu, Jul 29, 2021 at 10:29 AM Glasser, Matthew
> wrote:
>
> *External Email - Use Caution*
>
> I’m not sure anyone has tried this yet. Which data are you trying to
> analyze? I cannot tell from the below what type of data this is.
>
>
>
> Matt.
>
>
>
> *From: * on behalf of Poortata
> Shirish Lalwani
> *Reply-To: *Freesurfer support list
> *Date: *Thursday, July 29, 2021 at 10:23 AM
> *To: *Freesurfer support list
> *Subject: *[Freesurfer] Analysing HCP Data in freesurfer
>
> *External Email - Use Caution*
>
> Hello,
>
> I am trying to use fsfast to perform 1st level GLM
> analysis on preprocessed data from the HCP-Aging dataset which happens to
> be in a different space than fsaverage. I followed the following steps:
>
>
>
> First I smoothed the data which was in dtseries format
>
> wb_command -cifti-smoothing *dtseries.nii 1.27 1.27 COLUMN
> f.sm3.dtseries.nii -left-surface *L.midthickness_MSMAll.32k_fs_LR.surf.gii
> -right-surface
Re: [Freesurfer] Analysing HCP Data in freesurfer
External Email - Use Caution I am trying to analyse the HCP-Aging vismotor task fMRI data <https://secure-web.cisco.com/1Z30FmBulf3wPk8ZI1piszdCtNxfv_oM8hAju_21Q2rqxpYuGRsbRPC84dN3sp47oBdJLeOU7T9szqn8hcIkH4BhLhOBGhJvd5XLqntcuUFtPaWurM0LgbDUCjvps3yPQB_EvdAfv_Ao-NgAp8KZNUYyv4AybUV5-WXbC3PjGeQIaj7FgDLIVaKTIx1Snw558T4Vnz72IWqJurISu__OS0h5zc-uKdjgeB4bPhvloeUMkY57oe6VxBLQ93zhlWAyKpxdlrKxLcu1BnxApRJa6kA/https%3A%2F%2Fwww.humanconnectome.org%2Fstudy%2Fhcp-lifespan-aging%2Fproject-protocol%2Ftask-protocols-hcp-aging> with an event-based design. The provided file is dtseries.nii format and is the recommended starting point for tfMRI analyses by HCP-Aging. The cleaned file is precisely aligned across subjects using the MSMAll multimodal surface registration and is created applying GenericfMRIVolumeProcessingPipeline, GenericfMRISurfaceProcessingPipeline, hcp_fix_multi_run, and MSMAllPipeline. I was hoping to simply run GLM analysis on this file in fsfast but I am not sure which files the smoothing function is searching for since it is surface-based analysis. On Thu, Jul 29, 2021 at 10:29 AM Glasser, Matthew wrote: > External Email - Use Caution > > I’m not sure anyone has tried this yet. Which data are you trying to > analyze? I cannot tell from the below what type of data this is. > > > > Matt. > > > > *From: * on behalf of Poortata > Shirish Lalwani > *Reply-To: *Freesurfer support list > *Date: *Thursday, July 29, 2021 at 10:23 AM > *To: *Freesurfer support list > *Subject: *[Freesurfer] Analysing HCP Data in freesurfer > > *External Email - Use Caution* > > Hello, > > I am trying to use fsfast to perform 1st level GLM > analysis on preprocessed data from the HCP-Aging dataset which happens to > be in a different space than fsaverage. I followed the following steps: > > > > First I smoothed the data which was in dtseries format > > wb_command -cifti-smoothing *dtseries.nii 1.27 1.27 COLUMN > f.sm3.dtseries.nii -left-surface *L.midthickness_MSMAll.32k_fs_LR.surf.gii > -right-surface *R.midthickness_MSMAll.32k_fs_LR.surf.gii > > > > Then extracted the left/right surface and volume > > wb_command -cifti-separate f.sm3.dtseries.nii COLUMN -metric CORTEX_LEFT > f.L.func.gii -metric CORTEX_RIGHT f.R.func.gii -volume-all f.mni152.nii > > > > Followed by creating a mask for the subcortical analysis > > mri_binarize --i Atlas_ROIs.2.nii.gz --match 810111213 > 1617182628474950515253 5458 > 60 --o subcortmask.nii.gz; > > > > and creating a global mean .dat file. > > wb_command -cifti-stats f.sm3.dtseries.nii -reduce MEAN > > global.waveform.dat > > > > Then I tried to run GLM analysis using FSFast. The subcortical > analysis completes without errors, but I am having trouble with the > surfaces. > > > > Surprisingly, the error seems to be at the Smoothing ACF step because it > is trying to perform it on volume even though I have specified that > the analysis should be in surface space. Attached are the selx3 log file > and analysis info file. Is there something with the analysis specification > or in earlier conversion steps? I would appreciate any help with this. > > Thank you > > > > Best, > > Pia > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1SSrXHl7mS5o984_LQWJ-D3T_p3xzAmM1jegJfm6cc1xY1dwGnKGuziQw5XrdmkhU1HNeyf1rHJAF6Q1HRcbeS4fo3iRogAknA6OHnfyGOM4VKshhI1-c9hOHSwZe8n4Al7zHmpFR90kT2EUrAPzjS5ZADpDWGT_srXz5X22Mvwvbimr7KMyZrGANbnDOLCW-xzBu9qpzGfruNylYVxuj8y_Vjl-M4DtxCoCgeL7ZxWRakQBIAI61Ijqd8meWb3JpYJ3jNLAVo2-rW5Jd3mJvuw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Analysing HCP Data in freesurfer
External Email - Use Caution Hello, I am trying to use fsfast to perform 1st level GLM analysis on preprocessed data from the HCP-Aging dataset which happens to be in a different space than fsaverage. I followed the following steps: First I smoothed the data which was in dtseries format wb_command -cifti-smoothing *dtseries.nii 1.27 1.27 COLUMN f.sm3.dtseries.nii -left-surface *L.midthickness_MSMAll.32k_fs_LR.surf.gii -right-surface *R.midthickness_MSMAll.32k_fs_LR.surf.gii Then extracted the left/right surface and volume wb_command -cifti-separate f.sm3.dtseries.nii COLUMN -metric CORTEX_LEFT f.L.func.gii -metric CORTEX_RIGHT f.R.func.gii -volume-all f.mni152.nii Followed by creating a mask for the subcortical analysis mri_binarize --i Atlas_ROIs.2.nii.gz --match 810111213 1617182628474950515253 5458 60 --o subcortmask.nii.gz; and creating a global mean .dat file. wb_command -cifti-stats f.sm3.dtseries.nii -reduce MEAN > global.waveform.dat Then I tried to run GLM analysis using FSFast. The subcortical analysis completes without errors, but I am having trouble with the surfaces. Surprisingly, the error seems to be at the Smoothing ACF step because it is trying to perform it on volume even though I have specified that the analysis should be in surface space. Attached are the selx3 log file and analysis info file. Is there something with the analysis specification or in earlier conversion steps? I would appreciate any help with this. Thank you Best, Pia selxavg3.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using MRS voxel mask in freesurfer surface space
Thank you so much for your response. I tried the 3rd solution and used --trgsubject fsaverage and that works like a charm. Best, Pia On Tue, Jan 9, 2018 at 6:04 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > You probably set up the FSFAST analysis to sample onto the fsaverage > surface (in your mkanalysis-sess command). There are a couple of things > you can do: 1. redo the FSFAST analysis using "self" instead of > fsaverage. 2. map the beta.nii to the subject's native anatomy using > mri_surf2surf, or 3. Run mri_vol2surf with --trgsubject fsaverge to have > your MRS output in fsaverage space > > > On 01/09/2018 03:00 PM, Poortata Shirish Lalwani wrote: > > Hello Freesurfer experts, > > We are obtaining MRS data and functional MRI data on two separate days > > for each subject. We use structural scan obtained during both these > > sessions for the freesurfer segmentation. > > MRS scan gives us a binary mask (nii format) in the same space as the > > structural image obtained during that particular scan. We want to use > > this binary mask during the surface based functional MRI analysis. > > I tried the following process to do this: > > 1) Registered the structural image to orig.mgz using: > > bbregister --mov t1spgr.nii --s subject --t1 --init-fsl --reg > > register.dat > > 2) Applied the register.dat created by above process to the binary > > mask to transform it into the orig.mgz space using: > > mri_vol2vol --reg register.dat --mov gabarightxyz_mask.nii --fstarg > > --o gabarightmask.mgh --interp nearest > > (When I overlay this mask on orig.mgz using freeview they appear in > > the correct position.) > > 3) I then converted the volume to surface space using mri_vol2surf. > > mri_vol2surf --src gabarightmask.mgh --out gabarightsurf.nii --srcreg > > myregister.dat --hemi rh > > However the size of this mask created by mri_vol2surf process is > > (145236vertices) different from the size of beta.nii (163842 vertices) > > that is created using selxavg. Is one of the above steps wrong? How to > > resolve this discrepancy? > > > > Best, > > Pia > > > > On Mon, Jan 8, 2018 at 2:58 PM, Poortata Shirish Lalwani > > <poort...@umich.edu <mailto:poort...@umich.edu>> wrote: > > > > Hi, > > We are obtaining MRS data and functional MRI data on two separate > > days for each subject. We use structural scan obtained during both > > these sessions for the freesurfer segmentation. MRS scan gives us > > a binary mask (nii format) in the same space as the structural > > image obtained during that particular scan. We want to use this > > binary mask during the surface based functional MRI analysis. I am > > not sure how to transform this binary mask to the surface space. > > Is there a way to do this? > > > > Best, > > Pia > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Using MRS voxel mask in freesurfer surface space
Hello Freesurfer experts, We are obtaining MRS data and functional MRI data on two separate days for each subject. We use structural scan obtained during both these sessions for the freesurfer segmentation. MRS scan gives us a binary mask (nii format) in the same space as the structural image obtained during that particular scan. We want to use this binary mask during the surface based functional MRI analysis. I tried the following process to do this: 1) Registered the structural image to orig.mgz using: bbregister --mov t1spgr.nii --s subject --t1 --init-fsl --reg register.dat 2) Applied the register.dat created by above process to the binary mask to transform it into the orig.mgz space using: mri_vol2vol --reg register.dat --mov gabarightxyz_mask.nii --fstarg --o gabarightmask.mgh --interp nearest (When I overlay this mask on orig.mgz using freeview they appear in the correct position.) 3) I then converted the volume to surface space using mri_vol2surf. mri_vol2surf --src gabarightmask.mgh --out gabarightsurf.nii --srcreg myregister.dat --hemi rh However the size of this mask created by mri_vol2surf process is (145236 vertices) different from the size of beta.nii (163842 vertices) that is created using selxavg. Is one of the above steps wrong? How to resolve this discrepancy? Best, Pia On Mon, Jan 8, 2018 at 2:58 PM, Poortata Shirish Lalwani <poort...@umich.edu > wrote: > Hi, > We are obtaining MRS data and functional MRI data on two separate days for > each subject. We use structural scan obtained during both these sessions > for the freesurfer segmentation. MRS scan gives us a binary mask (nii > format) in the same space as the structural image obtained during that > particular scan. We want to use this binary mask during the surface based > functional MRI analysis. I am not sure how to transform this binary mask to > the surface space. Is there a way to do this? > > Best, > Pia > ___ 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] Using MRS voxel mask in freesurfer surface space
Hi, We are obtaining MRS data and functional MRI data on two separate days for each subject. We use structural scan obtained during both these sessions for the freesurfer segmentation. MRS scan gives us a binary mask (nii format) in the same space as the structural image obtained during that particular scan. We want to use this binary mask during the surface based functional MRI analysis. I am not sure how to transform this binary mask to the surface space. Is there a way to do this? Best, Pia ___ 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.
