Oh, you're using a task regressor? That will not be convolved with the
HRF (or its derivative). The HRF/deriv only applies to paradigm files.
If you want that in your task regressor, you will have to do it yourself.
On 6/7/2022 4:08 AM, Laura Doll wrote:
> External Email - Use Caution
>
> Yes, I think so. That would mean, that the additional frames correspond to
> the weights of the derivatives, right?
>
> But as I mentioned in the previous mail, they do have the same dimensions (in
> matlab, checking the beta.vol).
> Do you have any idea, what could have gone wrong?
> I double checked for Copy/Paste errors or stuff like that, but didn't find
> any.
>
> These are the exact terminal entries from last week:
>
> mkanalysis-sess -fsd bold -stc siemens -surface fsaverage lh -fwhm 5 -notask
> -spmhrf 1 -TR 2 -polyfit 2 -analysis TestPupAvg.lh -per-run -taskreg PupAvg 1
> selxavg3-sess -s S05 -analysis TestPupAvg.lh
> mkanalysis-sess -fsd bold -stc siemens -surface fsaverage lh -fwhm 5 -notask
> -spmhrf 0 -TR 2 -polyfit 2 -analysis Test0PupAvg.lh -per-run -taskreg PupAvg 1
> selxavg3-sess -s S05 -analysis Test0PupAvg.lh
>
> And I loaded the results in Matlab with
> beta1 = load_nifti('./S05/bold/TestPupAvg.lh/beta.nii.gz')
> beta0 = load_nifti('./S05/bold/Test0PupAvg.lh/beta.nii.gz')
>
> Which results in equal beta1 and beta0.
>
>
> Best,
> Laura
>
> Am Freitag, 03. Juni 2022 19:04 CEST, "Douglas N. Greve"
> <dgr...@mgh.harvard.edu> schrieb:
>
>> The -spmhrf 1 and 2 should have had additional frame in the beta.nii.gz.
>> Is that what you are looking at?
>>
>> On 6/3/2022 4:51 AM, Laura Doll wrote:
>>> External Email - Use Caution
>>>
>>> Okay, thanks.
>>> But how can I find out the influence of the derivatives used?
>>> I also tried to check the beta.nii.gz files for three different versions of
>>> the analysis (-spmhrf 0 1 and 2), assuming that the weights for the
>>> derivatives might be saved as additional dimensions, but the dimensions
>>> were the same for all (163842x1x1x10).
>>>
>>> I feel like I am missing something here, or maybe there is some mistake in
>>> my analysis?
>>> This is what I used:
>>>
>>> mkanalysis-sess -fsd bold -stc siemens -surface fsaverage lh -fwhm 5
>>> -notask -spmhrf 0 -TR 2 -polyfit 2 -analysis Test0.lh -per-run -taskreg
>>> PupAvg 1
>>>
>>> selxavg3-sess -s S05 -analysis Test0.lh
>>>
>>> And Test1/2 with -spmhrf 1/2, respectively.
>>>
>>> Thanks in Advance!
>>>
>>> Laura
>>>
>>>
>>> Am Mittwoch, 01. Juni 2022 16:50 CEST, "Douglas N. Greve"
>>> <dgr...@mgh.harvard.edu> schrieb:
>>>
>>>> It uses the default parameters:
>>>> tau1 = 1;
>>>> tau2 = 1;
>>>> ttp1 = 5*tau1; % 6 %
>>>> ttp2 = 15*tau1; % 16 %
>>>> c = 1/6;
>>>>
>>>>
>>>>
>>>> On 6/1/2022 4:27 AM, Laura Doll wrote:
>>>>> External Email - Use Caution
>>>>>
>>>>> Hi Doug,
>>>>>
>>>>> Thanks for your hint where to find the actual function.
>>>>> But how can I find which values were used in my analysis? I.e. the input
>>>>> to this function?
>>>>>
>>>>> Best,
>>>>> Laura
>>>>>
>>>>> Am Dienstag, 31. Mai 2022 17:19 CEST, "Douglas N. Greve"
>>>>> <dgr...@mgh.harvard.edu> schrieb:
>>>>>
>>>>>> Look here $FREESURFER/fsfast/toolbox/fast_spmhrf.m
>>>>>>
>>>>>> On 5/25/2022 9:19 AM, Laura Doll wrote:
>>>>>>> External Email - Use Caution
>>>>>>>
>>>>>>> Hi everyone,
>>>>>>>
>>>>>>> I need some help regarding the SPM-HRF with two derivatives:
>>>>>>> Where can I find the actual function that was used for the analysis? I
>>>>>>> am mostly interested in the peak latency, but would also appreciate if
>>>>>>> I can check the other parameters of the function somewhere.
>>>>>>>
>>>>>>> Best,
>>>>>>> Laura
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://secure-web.cisco.com/1xTlG-Uyb1U2QOCkOd7SM_GM-P5ioVq3Xn-ZIBk2jMCvLgt_ej_-0lwM9sGa6sE0VR22huqY8k28LeVc8UmVh9JhbA19F4S-KkN9jt-qw6MytIf9zcpxHr0Uq7jHznAs-mAgiAdqKv4ngbrpk6lr99ZeurunWbYUD4AwtyGo9qXW44fK2xyarNRcF_sVQfSfHN-abS3zKcgfeEPT0InC7ndMssP_m3gjlJjg8MKgY65KS-exNqCyu-qiCyjAZ4WFTanoXFuX47S_uHuMQwm4AqgaY5mb3fGJ0Ni09H6YoPtuieppduL6IslQTHZiKs1bn/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://secure-web.cisco.com/1xTlG-Uyb1U2QOCkOd7SM_GM-P5ioVq3Xn-ZIBk2jMCvLgt_ej_-0lwM9sGa6sE0VR22huqY8k28LeVc8UmVh9JhbA19F4S-KkN9jt-qw6MytIf9zcpxHr0Uq7jHznAs-mAgiAdqKv4ngbrpk6lr99ZeurunWbYUD4AwtyGo9qXW44fK2xyarNRcF_sVQfSfHN-abS3zKcgfeEPT0InC7ndMssP_m3gjlJjg8MKgY65KS-exNqCyu-qiCyjAZ4WFTanoXFuX47S_uHuMQwm4AqgaY5mb3fGJ0Ni09H6YoPtuieppduL6IslQTHZiKs1bn/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>>>>> 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://secure-web.cisco.com/1rmpvCcfVFDGqLo0LGNPuBTY2MFdv4E2_gcyoqa-EMXdV9p984n56GfiG-dDR5xhGNjnw9THCns8M8O3RiJdZNEMtAoax7dRt2gea4yOXlZee8KVoMNf1Zr7PkA2CTkxU3dRqm3TWU_FE7SO-g8Nj9wS8M97IHRnQHB2PxdVLjXKUTWxGbxHebcALbaQAztqB-otalJCPfKm_DOCCaMUSyBdPQiq6c12-zEBFFag7APhVCv2F2MCVBq7BiiKmgfg96x4p58F9EqYye4FmC1rv7YPaHU6EO6Wb1HTnles6k7xs59YwTPfDoGDj14oKEg1F/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>>>>>>
>>>>>> <https://secure-web.cisco.com/1rmpvCcfVFDGqLo0LGNPuBTY2MFdv4E2_gcyoqa-EMXdV9p984n56GfiG-dDR5xhGNjnw9THCns8M8O3RiJdZNEMtAoax7dRt2gea4yOXlZee8KVoMNf1Zr7PkA2CTkxU3dRqm3TWU_FE7SO-g8Nj9wS8M97IHRnQHB2PxdVLjXKUTWxGbxHebcALbaQAztqB-otalJCPfKm_DOCCaMUSyBdPQiq6c12-zEBFFag7APhVCv2F2MCVBq7BiiKmgfg96x4p58F9EqYye4FmC1rv7YPaHU6EO6Wb1HTnles6k7xs59YwTPf
>>>>>
>>>>> DoGDj14oKEg1F/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
>>>>>
>>>>>> 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.
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://secure-web.cisco.com/15MwAfVGnUqKN7rT-xVNnq5illbu0B1pfauCA2TYbEqzDMt5O7fHqwM3-iQoZtS16m_5GOuyWc83c52VvQ1L2nKR3stQ4PVgxnoRWmfEmG5uVSqpndch_2sNZj4G7qMFdmonAsyRE1pBDmvnmDk50MOU2Bkh5u5o5U2AZOu6aIDqgZpph7JixJg3xnRHaLRJokdGRbT_Zce9aC7b0UwEMVD58KkaT6t9rhZ2EwCcZgnf8cYIHTyhItI6An8azQrk4AchW44wGcTBTeo7I3xIFmN6dP5mskg96-bMw4iIJHrGOvfsnc0BioHv74pNDVrHo_eHPtRyJVT7MuiZgCRBJ8A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://secure-web.cisco.com/15MwAfVGnUqKN7rT-xVNnq5illbu0B1pfauCA2TYbEqzDMt5O7fHqwM3-iQoZtS16m_5GOuyWc83c52VvQ1L2nKR3stQ4PVgxnoRWmfEmG5uVSqpndch_2sNZj4G7qMFdmonAsyRE1pBDmvnmDk50MOU2Bkh5u5o5U2AZOu6aIDqgZpph7JixJg3xnRHaLRJokdGRbT_Zce9aC7b0UwEMVD58KkaT6t9rhZ2EwCcZgnf8cYIHTyhItI6An8azQrk4AchW44wGcTBTeo7I3xIFmN6dP5mskg96-bMw4iIJHrGOvfsnc0BioHv74pNDVrHo_eHPtRyJVT7MuiZgCRBJ8A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>>> 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://secure-web.cisco.com/1Qi6ElK_fjwy94vTv9KiwGpNGl5QMcdQzbSns5CIjq6mQ44BAWGxf63iTdPnaCZ0LkVKH311ogF5O6ZA-rF971EqNKoWeHTM93SCcVtIn01Sxg0dCYhHl2tlXU938vqq5jlYTziCepyG0dUdnEHItOR5zp_fU9ROlOjFFFgKZ_n7YazucEXrUxXROw0mlnKWD65v-WUrnRYy2L2PU0Tlyi0LxAk053Ny2MaF2p_QUQidauy5wYvnnhXsF35znryY7ciDHViJyBIBJrjnTj6Rz8RDpBlqvWJREVtByG90qiQQ1BFXgZCIWffA2qC97B8NvZMARl57SKWku-ztHitAB6w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>>>>
>>>> <https://secure-web.cisco.com/1Qi6ElK_fjwy94vTv9KiwGpNGl5QMcdQzbSns5CIjq6mQ44BAWGxf63iTdPnaCZ0LkVKH311ogF5O6ZA-rF971EqNKoWeHTM93SCcVtIn01Sxg0dCYhHl2tlXU938vqq5jlYTziCepyG0dUdnEHItOR5zp_fU9ROlOjFFFgKZ_n7YazucEXrUxXROw0mlnKWD65v-WUrnRYy2L2PU0Tlyi0LxAk053Ny2MaF2p_QUQidauy5wYvnnhXsF35znryY7ciDHViJyBIBJrjnTj6Rz8RDpBlqvWJREVtByG90qiQQ1BFXgZCIWffA2qC97B8NvZMARl57SKWku-ztHitAB6w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>>>> .
>>>> 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.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://secure-web.cisco.com/1uo6vLb4Q6MLQLyMzD9STPjsMURZqYlgZ5dGWV8bqF_UmvbzcMflrYt4E0vdxaRd2XE06fLZGGECyuLD3E-Sij0PI9c9DV_1K7LTfRgV1i7UHbUsxfpVFP6HwUpaTF7x2qj7X67cDfBnskFe-iu6ck7F1BztYAtnZkRyZhb9vs-ChoUGf-T3-OefeOILK0PHLBNBh2RyGKo1g0rrKSSOQLfJ1pvQ17Q5RIb8ZOGIalgnttbtQX-MqhFHlBy1stsKmDi-BGY7Q_XXDfvbWbIFVdrWsBgpMJn8R6EI0PP56riK3MadSTiKNV6vbDYwhTGh0RAPs5CZbF1nhh8pHUeRV2A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://secure-web.cisco.com/1uo6vLb4Q6MLQLyMzD9STPjsMURZqYlgZ5dGWV8bqF_UmvbzcMflrYt4E0vdxaRd2XE06fLZGGECyuLD3E-Sij0PI9c9DV_1K7LTfRgV1i7UHbUsxfpVFP6HwUpaTF7x2qj7X67cDfBnskFe-iu6ck7F1BztYAtnZkRyZhb9vs-ChoUGf-T3-OefeOILK0PHLBNBh2RyGKo1g0rrKSSOQLfJ1pvQ17Q5RIb8ZOGIalgnttbtQX-MqhFHlBy1stsKmDi-BGY7Q_XXDfvbWbIFVdrWsBgpMJn8R6EI0PP56riK3MadSTiKNV6vbDYwhTGh0RAPs5CZbF1nhh8pHUeRV2A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> 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://secure-web.cisco.com/18o8QQM2Y6H0aKvdfjmx4Qax2XPYOX4eW3yOTMRwMgt2i_acK_Pp8bLjeoQM6tDbY8AkzyMTimq8yIw8VWD1QAcw_o5MolcTTlfBoQtr8fHzlTqxKi0y9PVntYP0kC_L7rdoFHJWQtCdV4O7aNv3aAYcZv2GCzJtAoTVI3dn1RjWpkOo24FezI_ScxskNUo6sLi2-UaORrMoqJbSEptxO4LO5OTS0LhgIoZToQyL7AUuNisnUQuGp2y-wG9EIgbVmSzHwDaYK1eqfx_rwiDzyCN2j4P6AYW-qmZPqqELZhjQt_7G3pGc_4jMR_x8DMix5VCo4nmXVPFKKyugPSqBU7Q/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>>
>> <https://secure-web.cisco.com/18o8QQM2Y6H0aKvdfjmx4Qax2XPYOX4eW3yOTMRwMgt2i_acK_Pp8bLjeoQM6tDbY8AkzyMTimq8yIw8VWD1QAcw_o5MolcTTlfBoQtr8fHzlTqxKi0y9PVntYP0kC_L7rdoFHJWQtCdV4O7aNv3aAYcZv2GCzJtAoTVI3dn1RjWpkOo24FezI_ScxskNUo6sLi2-UaORrMoqJbSEptxO4LO5OTS0LhgIoZToQyL7AUuNisnUQuGp2y-wG9EIgbVmSzHwDaYK1eqfx_rwiDzyCN2j4P6AYW-qmZPqqELZhjQt_7G3pGc_4jMR_x8DMix5VCo4nmXVPFKKyugPSqBU7Q/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> .
>> 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.
>
>
>
>
>
>
>
> _______________________________________________
> 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 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.
