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 glasserm@wustl.edu 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: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Poortata Shirish Lalwani poortata@umich.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, July 29, 2021 at 10:23 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *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 8 10 11 12 13 16 17 18 26 28 47 49 50 51 52 53 54 58 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_p3xzAmM1jegJfm6cc1xY1d...

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 glasserm@wustl.edu 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: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Poortata Shirish Lalwani poortata@umich.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, July 29, 2021 at 11:39 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *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 glasserm@wustl.edu 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: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Poortata Shirish Lalwani poortata@umich.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, July 29, 2021 at 10:23 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *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 8 10 11 12 13 16 17 18 26 28 47 49 50 51 52 53 54 58 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.

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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/1kWAAhc7SK1awvrmo122jmSnBdVVhZQ7wJCDrJm4mw7Kx6V...

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: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Glasser, Matthew" glasserm@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, July 30, 2021 at 7:43 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu 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/1Kx4v4Z0ry1cLWDjWWA0GB-gQ-GbOk7O82thSRoypDsSzhJ...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: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Poortata Shirish Lalwani poortata@umich.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, July 30, 2021 at 7:43 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu 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 <glasserm@wustl.edumailto:glasserm@wustl.edu> 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: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Poortata Shirish Lalwani <poortata@umich.edumailto:poortata@umich.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, July 29, 2021 at 11:39 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Analysing HCP Data in freesurfer

External Email - Use Caution I am trying to analyse the HCP-Aging vismotor task fMRI datahttps://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 <glasserm@wustl.edumailto:glasserm@wustl.edu> 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: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Poortata Shirish Lalwani <poortata@umich.edumailto:poortata@umich.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, July 29, 2021 at 10:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> 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 8 10 11 12 13 16 17 18 26 28 47 49 50 51 52 53 54 58 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.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1S_z8dmoO610bFtU6flkMOBIo-NuCXJWhICXVIxerqlAvVt...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

________________________________ 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.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1S_z8dmoO610bFtU6flkMOBIo-NuCXJWhICXVIxerqlAvVt...https://secure-web.cisco.com/1kWAAhc7SK1awvrmo122jmSnBdVVhZQ7wJCDrJm4mw7Kx6Vhc42DUbUfYtfgyKU4Z66DCb0V3OW6iKiCEs1Z-oAlNgAC5TQj0uHxgCyR76cZYg6CZCTDOO9-AwDdmGAhYmXhk_tc2OBmv8Kgo4YgQoc7ULdCmFqV1tqgbeuYiP8cp4LlFtZwpzOQNvj2mZNmsd9JtiJWKq_sPfY0SJCc2pFFXUQ4gUrStdU8mW1eIhCnA_V0LxJ70dgjpC_AcH0jbVp1uqZqNId-nsHvy9bxoUA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

________________________________ 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.

________________________________ 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.

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 poortata@umich.edu wrote:

Thanks Matt. That is super helpful!!

On Fri, Jul 30, 2021 at 1:40 PM Glasser, Matthew glasserm@wustl.edu 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: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Glasser, Matthew" glasserm@wustl.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, July 30, 2021 at 7:43 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *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-Tyy8mtEKvEhCuDvWPcrpsJ... 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: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Poortata Shirish Lalwani poortata@umich.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, July 30, 2021 at 7:43 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Analysing HCP Data in freesurfer

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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 glasserm@wustl.edu wrote:

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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: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Poortata Shirish Lalwani poortata@umich.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, July 29, 2021 at 11:39 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Analysing HCP Data in freesurfer

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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 glasserm@wustl.edu wrote:

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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: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Poortata Shirish Lalwani poortata@umich.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, July 29, 2021 at 10:23 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Analysing HCP Data in freesurfer

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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 8 10 11 12 13 16 17 18 26 28 47 49 50 51 52 53 54 58 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

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